Btk inhibitors for the treatment of cns malignancies

ABSTRACT

Described herein are irreversible Btk inhibitor compounds, and methods for using such irreversible inhibitors in the treatment of CNS malignancies.

RELATED APPLICATIONS

The present application claims the benefit of priority from U.S. Provisional Application Nos. 62/024,457, filed Jul. 14, 2014, 62/030,023, filed Jul. 28, 2014, and 62/052,394, filed Sep. 18, 2014, which are herein incorporated by reference in their entirety.

BACKGROUND OF THE INVENTION

Cancer of the central nervous system (CNS), include among other things the brain, meninges and spinal cord. The seriousness and treatability of primary brain malignancies is determined by a number of variables including histology, size of tumor, extent of the malignancy, the patient's age and performance status, and the duration of symptoms. Some primary brain tumors are curable by surgery alone, or by surgery and radiation therapy combined; but the remainder are not usually curable despite all the therapies combined.

SUMMARY OF THE INVENTION

Disclosed herein, in certain embodiments, are methods for treating a CNS malignancy in an individual in need thereof comprising administering to an individual in need thereof a composition comprising a therapeutically-effective amount of (R)-1-(3-(4-amino-3-(4-phenoxyphenyl)-1H-pyrazolo[3,4-d]pyrimidin-1-yl)piperidin-1-yl)prop-2-en-1-one

Described herein, in certain embodiments, are methods for treating a disorder characterized by the presence or development of one or more CNS malignancies comprising administering to an individual in need a pharmaceutical formulation comprising a compound of Formula (A1) having the structure:

Wherein:

A is independently selected from N or CR₅; R₁ is H, L₂-(substituted or unsubstituted alkyl), L₂-(substituted or unsubstituted cycloalkyl), L₂-(substituted or unsubstituted alkenyl), L₂-(substituted or unsubstituted cycloalkenyl), L₂-(substituted or unsubstituted heterocycle), L₂-(substituted or unsubstituted heteroaryl), or L₂-(substituted or unsubstituted aryl), where L₂ is a bond, O, S, —S(═O), —S(═O)₂, C(═O), -(substituted or unsubstituted C₁-C₆ alkylene), or -(substituted or unsubstituted C₂-C₆ alkenylene); R₂ and R₃ are independently selected from H, lower alkyl and substituted lower alkyl; R₄ is L₃-X-L₄-G, wherein, L₃ is optional, and when present is a bond, or an optionally substituted group selected from alkylene, heteroalkylene, arylene, heteroarylene, alkylarylene, alkylheteroarylene, or alkylheterocycloalkylene; X is optional, and when present is a bond, O, —C(═O), S, —S(═O), —S(═O)₂, —NH, —NR₉, —NHC(O), —C(O)NH, —NR₉C(O), —C(O)NR₉, —S(═O)₂NH, —NHS(═O)₂, —S(═O)₂NR₉—, —NR₉S(═O)₂, —OC(O)NH—, —NHC(O)O—, —OC(O)NR₉—, —NR₉C(O)O—, —CH═NO—, —ON═CH—, —NR₁₀C(O)NR₁₀—, heteroarylene, arylene, —NR₁₀C(═NR₁₁)NR₁₀—, —NR₁₀C(═NR₁₁)—, —C(═NR₁₁)NR₁₀—, —OC(═NR₁₁)—, or —C(═NR₁₁)O—; L₄ is optional, and when present is a bond, substituted or unsubstituted alkylene, substituted or unsubstituted cycloalkylene, substituted or unsubstituted alkenylene, substituted or unsubstituted alkynylene, substituted or unsubstituted arylene, substituted or unsubstituted heteroarylene, substituted or unsubstituted heterocyclene; or L₃, X and L₄ taken together form a nitrogen containing heterocyclic ring, or an optionally substituted group selected from alkyl, heteroalkyl, aryl, heteroaryl, alkylaryl, alkylheteroaryl, or alkylheterocycloalkyl;

G is

where R^(b) is H, substituted or unsubstituted alkyl, substituted or unsubstituted cycloalkyl; and either

R₇ and R₈ are H;

R₆ is H, substituted or unsubstituted C₁-C₄alkyl, substituted or unsubstituted C₁-C₄heteroalkyl, C₁-C₈ alkylaminoalkyl, C₁-C₈hydroxyalkylaminoalkyl, C₁-C₈ alkoxyalkylaminoalkyl, substituted or unsubstituted C₃-C₆cycloalkyl, substituted or unsubstituted C₁-C₈alkylC₃-C₆cycloalkyl, substituted or unsubstituted aryl, substituted or unsubstituted C₂-C₈heterocycloalkyl, substituted or unsubstituted heteroaryl, C₁-C₄alkyl (aryl), C₁-C₄alkyl (heteroaryl), C₁-C₈ alkylethers, C₁-C₈ alkylamides, or C₁-C₄alkyl (C₂-C₈heterocycloalkyl); or

R₆ and R₈ are H;

R₇ is H, substituted or unsubstituted C₁-C₄alkyl, substituted or unsubstituted C₁-C₄heteroalkyl, C₁-C₈ alkylaminoalkyl, C₁-C₈hydroxyalkylaminoalkyl, C₁-C₈ alkoxyalkylaminoalkyl, substituted or unsubstituted C₃-C₆cycloalkyl, substituted or unsubstituted C₁-C₈alkylC₃-C₆cycloalkyl, substituted or unsubstituted aryl, substituted or unsubstituted C₂-C₈heterocycloalkyl, substituted or unsubstituted heteroaryl, C₁-C₄alkyl(aryl), C₁-C₄alkyl(heteroaryl), C₁-C₈alkylethers, C₁-C₈ alkylamides, or C₁-C₄alkyl (C₂-C₈heterocycloalkyl); or R₇ and R₈ taken together form a bond; R₆ is H, substituted or unsubstituted C₁-C₄alkyl, substituted or unsubstituted C₁-C₄heteroalkyl, C₁-C₈alkylaminoalkyl, C₁-C₈hydroxyalkylaminoalkyl, C₁-C₈alkoxyalkylaminoalkyl, substituted or unsubstituted C₃-C₆cycloalkyl, substituted or unsubstituted C₁-C₈alkylC₃-C₆cycloalkyl, substituted or unsubstituted aryl, substituted or unsubstituted C₂-C₈heterocycloalkyl, substituted or unsubstituted heteroaryl, C₁-C₄alkyl(aryl), C₁-C₄alkyl(heteroaryl), C₁-C₈alkylethers, C₁-C₈alkylamides, or C₁-C₄alkyl(C₂-C₈heterocycloalkyl); R₅ is H, halogen, -L₆-(substituted or unsubstituted C₁-C₃ alkyl), -L₆-(substituted or unsubstituted C₂-C₄ alkenyl), -L₆-(substituted or unsubstituted heteroaryl), or -L₆-(substituted or unsubstituted aryl), wherein L₆ is a bond, O, S, —S(═O), S(═O)₂, NH, C(O), —NHC(O)O, —OC(O)NH, —NHC(O), or —C(O)NH; R₉ is selected from among H, substituted or unsubstituted lower alkyl, and substituted or unsubstituted lower cycloalkyl; each R₁₀ is independently H, substituted or unsubstituted lower alkyl, or substituted or unsubstituted lower cycloalkyl; or two R₁₀ groups can together form a 5-, 6-, 7-, or 8-membered heterocyclic ring; or R₁₀ and R₁₁ can together form a 5-, 6-, 7-, or 8-membered heterocyclic ring; or R₁₁ is selected from H, —S(═O)₂R₈, —S(═O)₂NH₂, —C(O)R₈, —CN, —NO₂, heteroaryl, or heteroalkyl; and pharmaceutically active metabolites, pharmaceutically acceptable solvates, pharmaceutically acceptable salts, or pharmaceutically acceptable prodrugs thereof.

In some embodiments R₁ is L₂-(substituted or unsubstituted aryl), and L₂ is a bond.

In some embodiments L₃, X and L₄ taken together form a nitrogen containing heterocyclic ring.

In some embodiments G is

Described herein methods of treating a CNS malignancy in an individual in need thereof comprising administering to the individual a composition comprising a therapeutically-effective amount of an ACK (Accessible Cysteine Kinase) inhibitor compound (e.g., a Btk inhibitor, such as for example ibrutinib). In some embodiments the ACK inhibitor compound is a Btk inhibitor compound. In some embodiments, the ACK inhibitor compound is (R)-1-(3-(4-amino-3-(4-phenoxyphenyl)-1H-pyrazolo[3,4-d]pyrimidin-1-yl)piperidin-1-yl)prop-2-en-1-one (i.e. PCI-32765/ibrutinib).

Described herein, in certain embodiments, are methods for detecting and measuring a Btk inhibitor level in human CNS fluid, comprising:

-   -   a. obtaining a cerebrospinal fluid (CSF) sample; and     -   b. measuring the level of the Btk inhibitor from the CSF sample         thereby determining the amount of the Btk inhibitor present in         the CNS fluid.

In some embodiments the measuring the level of the Btk inhibitor from the CSF sample is performed using liquid chromatography-tandem mass spectroscopy. In some embodiments, the method further comprising centrifuging the CSF sample to obtain a supernatant portion and adding an internal standard to the supernatant portion of the CSF sample prior to analysis.

In some embodiments the method, further comprises:

-   -   a. integrating the area-under-the curve for a peak of the Btk         inhibitor from a plot of signal intensity as a function of         elution time from the liquid chromatography-tandem mass         spectroscopy;     -   b. integrating the area-under-the curve for a peak of the         internal standard from the plot of signal intensity as a         function of elution time from the liquid chromatography-tandem         mass spectroscopy;     -   c. determining a ratio by dividing the resultant integration         from step b by the resultant integration from step a;     -   d. providing a standard calibration curve; and     -   e. calculating the concentration of the Btk inhibitor in the CSF         sample by using a power fit regression formula without         weighting.

In some embodiments the slope and intercept are calculated from the standard calibration curve.

In some embodiments the Btk inhibitor is ibrutinib (PCI-32765). In some embodiments the Btk inhibitor is PCI-45227.

In some embodiments the internal standard for ibrutinib is d5-PCI-32765. In some embodiments the internal standard for PCI-45227 is d5-PCI-45227.

In some embodiments the detection range of the Btk inhibitor in the CSF sample is from about 0.01 ng/mL to about 50 ng/mL. In some embodiments the detection range of the Btk inhibitor in the CSF sample is from about 0.1 ng/mL to about 20 ng/mL. In some embodiments the detection range of the Btk inhibitor in the CSF sample is from about 0.3 ng/mL to about 10 ng/mL.

In some embodiments the liquid chromatography is a high-performance liquid chromatography (HPLC).

In some embodiments the CSF sample is a stored CSF sample or a fresh CSF sample. In some embodiments the stored CSF sample is a CSF sample stored on ice for at least 2 hours. In some embodiments the stored CSF sample is a CSF sample stored at −70±5° C. for at least 7 days.

In some embodiments the method further comprises processing a plasma sample to determine the concentration of the Btk inhibitor in the plasma sample, thereby providing an indication of the amount of the Btk inhibitor remaining in the plasma.

In some embodiments the detection range of the Btk inhibitor in the plasma sample is from about 1 ng/mL to about 1000 ng/mL.

Described herein, are methods for treating a CNS malignancy in an individual in need thereof, comprising:

-   -   a. administering to the individual a treatment comprising a         therapeutically effective amount of a Btk inhibitor; and     -   b. monitoring the progress of the treatment by measuring the         level of the Btk inhibitor present in CNS fluid.

In some embodiments the level of the Btk inhibitor is measured from a CSF sample, thereby determining the amount of the Btk inhibitor present in the CNS fluid.

In some embodiments the method further comprises measuring the level of the Btk inhibitor in the plasma, thereby additionally monitoring the progress of the treatment through the level of the Btk inhibitor remaining in the plasma.

In some embodiments the Btk inhibitor is ibrutinib (PCI-32765). In some embodiments the Btk inhibitor is PCI-45227.

In some embodiments the measuring of the level of the Btk inhibitor from the CSF sample is performed using liquid chromatography-tandem mass spectroscopy.

In some embodiments the method further comprises centrifuging the CSF sample to obtain a supernatant portion and adding an internal standard to the supernatant portion of the CSF sample prior to analysis.

In some embodiments the method further comprises:

-   -   a. integrating the area-under-the curve for a peak of the Btk         inhibitor from a plot of signal intensity as a function of         elution time from the liquid chromatography-tandem mass         spectroscopy;     -   b. integrating the area-under-the curve for a peak of the         internal standard from the plot of signal intensity as a         function of elution time from the liquid chromatography-tandem         mass spectroscopy;     -   c. determining a ratio by dividing the resultant integration         from step b by the resultant integration from step a;     -   d. providing a standard calibration curve; and     -   e. calculating the concentration of the Btk inhibitor in the CSF         sample by using a power fit regression formula without         weighting.

In some embodiments the slope and intercept are calculated from the standard calibration curve.

In some embodiments the internal standard for ibrutinib is d5-PCI-32765. In some embodiments the internal standard for PCI-45227 is d5-PCI-45227.

In some embodiments the detection range of the Btk inhibitor in the CSF sample is from about 0.01 ng/mL to about 50 ng/mL. In some embodiments the detection range of the Btk inhibitor in the CSF sample is from about 0.1 ng/mL to about 20 ng/mL. In some embodiments the detection range of the Btk inhibitor in the CSF sample is from about 0.3 ng/mL to about 10 ng/mL. In some embodiments the detection range of the Btk inhibitor in the plasma sample is from about 1 ng/mL to about 1000 ng/mL.

In some embodiments the liquid chromatography is a high-performance liquid chromatography (HPLC).

In some embodiments the CSF sample is a stored CSF sample or a fresh CSF sample. In some embodiments the stored CSF sample is a CSF sample stored on ice for at least 2 hours. In some embodiments the stored CSF sample is a CSF sample stored at −70±5° C. for at least 7 days.

In some embodiments the CNS malignancy is a primary CNS lymphoma. In some embodiments the primary CNS lymphoma is a glioma. In some embodiments the glioma is astrocytomas, ependymomas, oligodendrogliomas. In some embodiments the CNS malignancy is astrocytic tumors such as juvenile pilocytic, subependymal, well differentiated or moderately differentiated anaplastic astrocytoma; anaplastic astrocytoma; glioblastoma multiforme; ependymal tumors such as myxopapillary and well-differentiated ependymoma, anaplastic ependymoma, ependymoblastoma; oligodendroglial tumors including well-differentiated oligodendroglioma and anaplastic oligodendroglioma; mixed tumors such as mixed astrocytoma-ependymoma, mixed astrocytoma-oligodendroglioma, mixed astrocytomaependymoma-oligodendroglioma; or medulloblastoma.

In some embodiments the CNS malignancy is glioblastoma multiforme. In some embodiments the CNS malignancy is a secondary CNS lymphoma.

In some embodiments the level of the Btk inhibitor is measured before, during, or after administering to the individual the treatment comprising a therapeutically effective amount of the Btk inhibitor. In some embodiments the level of the Btk inhibitor is measured one, two, three, or more times during the course of the treatment.

In some embodiments the Btk inhibitor is administered once a day, two times per day, three times per day, four times per day, or five times per day.

In some embodiments the Btk inhibitor is administered at a dosage of about 40 mg/day to about 1000 mg/day. In some embodiments the Btk inhibitor is administered orally.

In some embodiments the method further comprises administering a second anti-cancer agent.

In some embodiments the ACK inhibitor compound (e.g., a Btk inhibitor, such as for example ibrutinib) is administered before, during or after the development of the CNS malignancy. In some embodiments, the ACK inhibitor compound (e.g., a Btk inhibitor, such as for example ibrutinib) is used as a prophylactic and is administered continuously to subjects with a propensity to develop a CNS malignancy. In some embodiments, the ACK inhibitor compound (e.g., a Btk inhibitor, such as for example ibrutinib) is administered to an individual during or as soon as possible after the development of a CNS malignancy. In some embodiments, the administration of the ACK inhibitor compound (e.g., a Btk inhibitor, such as for example ibrutinib) is initiated within the first 48 hours of the onset of the symptoms, within the first 6 hours of the onset of the symptoms, or within 3 hours of the onset of the symptoms. In some embodiments, the initial administration of the ACK inhibitor compound (e.g., a Btk inhibitor, such as for example ibrutinib) is via any route practical, such as, for example, an intravenous injection, a bolus injection, infusion over 5 minutes to about 5 hours, a pill, a capsule, transdermal patch, buccal delivery, and the like, or combination thereof. In some embodiments the ACK inhibitor compound (e.g., a Btk inhibitor, such as for example ibrutinib) should be administered as soon as is practicable after the onset of a disorder is detected or suspected, and for a length of time necessary for the treatment of the disease, such as, for example, from about 1 month to about 3 months. The length of treatment can vary for each subject, and the length can be determined using the known criteria. In some embodiments, the ACK inhibitor compound (e.g., a Btk inhibitor, such as for example ibrutinib) is administered for at least 2 weeks, between about 1 month to about 5 years, or from about 1 month to about 3 years.

In some embodiments the therapeutically effective amounts will depend on the severity and course of the disorder, previous therapy, the patient's health status, weight, and response to the drugs, and the judgment of the treating physician. Prophylactically effective amounts depend on the patient's state of health, weight, the severity and course of the disease, previous therapy, response to the drugs, and the judgment of the treating physician.

In some embodiments, the ACK inhibitor compound (e.g., a Btk inhibitor, such as for example ibrutinib) is administered to the patient on a regular basis, e.g., three times a day, two times a day, once a day, every other day or every 3 days. In other embodiments, the ACK inhibitor compound (e.g., a Btk inhibitor, such as for example ibrutinib) is administered to the patient on an intermittent basis, e.g., twice a day followed by once a day followed by three times a day; or the first two days of every week; or the first, second and third day of a week. In some embodiments, intermittent dosing is as effective as regular dosing. In further or alternative embodiments, the ACK inhibitor compound (e.g., a Btk inhibitor, such as for example ibrutinib) is administered only when the patient exhibits a particular symptom, e.g., the onset of pain, or the onset of a fever, or the onset of an inflammation, or the onset of a skin disorder. Dosing schedules of each compound may depend on the other or may be independent of the other.

In the case wherein the patient's condition does not improve, upon the doctor's discretion the administration of the compounds may be administered chronically, that is, for an extended period of time, including throughout the duration of the patient's life in order to ameliorate or otherwise control or limit the symptoms of the patient's disorder.

In the case wherein the patient's status does improve, upon the doctor's discretion the administration of the compounds may be given continuously; alternatively, the dose of drug being administered may be temporarily reduced or temporarily suspended for a certain length of time (i.e., a “drug holiday”). The length of the drug holiday can vary between 2 days and 1 year, including by way of example only, 2 days, 3 days, 4 days, 5 days, 6 days, 7 days, 10 days, 12 days, 15 days, 20 days, 28 days, 35 days, 50 days, 70 days, 100 days, 120 days, 150 days, 180 days, 200 days, 250 days, 280 days, 300 days, 320 days, 350 days, or 365 days. The dose reduction during a drug holiday may be from 10%-100%, including, by way of example only, 10%, 15%, 20%, 25%, 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, or 100%.

Once improvement of the patient's conditions has occurred, a maintenance regimen is administered if necessary. Subsequently, the dosage or the frequency of administration, or both, of the ACK inhibitor compound (e.g., a BTK inhibitor, such as for example ibrutinib) can be reduced, as a function of the symptoms, to a level at which the individual's improved condition is retained. Individuals can, however, require intermittent treatment on a long-term basis upon any recurrence of symptoms.

In some embodiments the amount of the ACK inhibitor compound (e.g., a Btk inhibitor, such as for example ibrutinib) will vary depending upon factors such as the particular compound, disorder and its severity, the identity (e.g., weight) of the subject or host in need of treatment, and is determined according to the particular circumstances surrounding the case, including, e.g., the specific agents being administered, the routes of administration, and the subject or host being treated. In general, however, doses employed for adult human treatment will typically be in the range of 0.02-5000 mg per day, or from about 1-1500 mg per day. The desired dose may be presented in a single dose or as divided doses administered simultaneously (or over a short period of time) or at appropriate intervals, for example as two, three, four or more sub-doses per day.

In some embodiments, the therapeutic amount of the ACK inhibitor (e.g., a Btk inhibitor, such as for example ibrutinib) is from 100 mg/day up to, and including, 2000 mg/day. In some embodiments, the amount of the ACK inhibitor (e.g., a Btk inhibitor, such as for example ibrutinib) is from 140 mg/day up to, and including, 840 mg/day. In some embodiments, the amount of the ACK inhibitor (e.g., a Btk inhibitor, such as for example ibrutinib) is from 420 mg/day up to, and including, 840 mg/day. In some embodiments, the amount of the ACK inhibitor (e.g., a Btk inhibitor, such as for example ibrutinib) is about 140 mg/day. In some embodiments, the amount of the ACK inhibitor (e.g., a Btk inhibitor, such as for example ibrutinib) is about 280 mg/day. In some embodiments, the amount of the ACK inhibitor (e.g., a Btk inhibitor, such as for example ibrutinib) is about 420 mg/day. In some embodiments, the amount of the ACK inhibitor (e.g., a Btk inhibitor, such as for example ibrutinib) is about 560 mg/day. In some embodiments, the amount of the ACK inhibitor (e.g., a Btk inhibitor, such as for example ibrutinib) is about 700 mg/day. In some embodiments, the amount of the ACK inhibitor (e.g., a Btk inhibitor, such as for example ibrutinib) is about 840 mg/day. In some embodiments, the amount of the ACK inhibitor (e.g., a Btk inhibitor, such as for example ibrutinib) is about 980 mg/day. In some embodiments, the amount of the ACK inhibitor (e.g., a Btk inhibitor, such as for example ibrutinib) is about 1120 mg/day. In some embodiments, the amount of the ACK inhibitor (e.g., a Btk inhibitor, such as for example ibrutinib) is about 1260 mg/day. In some embodiments, the amount of the ACK inhibitor (e.g., a BTK inhibitor, such as for example ibrutinib) is about 1400 mg/day.

In some embodiments, the dosage of the ACK inhibitor (e.g., a Btk inhibitor, such as for example ibrutinib) is escalated over time. In some embodiments, the dosage of the ACK inhibitor (e.g., a Btk inhibitor, such as for example ibrutinib) is escalated from at or about 1.25 mg/kg/day to at or about 12.5 mg/kg/day over a predetermined period of time. In some embodiments the predetermined period of time is over 1 month, over 2 months, over 3 months, over 4 months, over 5 months, over 6 months, over 7 months, over 8 months, over 9 months, over 10 months, over 11 months, over 12 months, over 18 months, over 24 months or longer.

In some embodiments the ACK inhibitor compound (e.g., a Btk inhibitor, such as for example ibrutinib) may be formulated into unit dosage forms suitable for single administration of precise dosages. In unit dosage form, the formulation is divided into unit doses containing appropriate quantities of one or both compounds. The unit dosage may be in the form of a package containing discrete quantities of the formulation. Non-limiting examples are packaged tablets or capsules, and powders in vials or ampoules. Aqueous suspension compositions can be packaged in single-dose non-reclosable containers. Alternatively, multiple-dose reclosable containers can be used, in which case it is typical to include a preservative in the composition. By way of example only, formulations for parenteral injection may be presented in unit dosage form, which include, but are not limited to ampoules, or in multi-dose containers, with an added preservative.

It is understood that a medical professional will determine the dosage regimen in accordance with a variety of factors. These factors include the CNS malignacy from which the subject suffers, the degree of metastasis, as well as the age, weight, sex, diet, and medical condition of the subject.

Described herein, in certain embodiments, are methods for treating a disorder characterized by the presence or development of one or more CNS malignancies comprising administering to an individual in need a pharmaceutical formulation comprising a Btk inhibitor.

In some embodiments the CNS malignancy is a primary CNS lymphoma. In some embodiments the primary CNS lymphoma is a glioma. In some embodiments the glioma is astrocytomas, ependymomas, oligodendrogliomas. In some embodiments the CNS malignancy is astrocytic tumors such as juvenile pilocytic, subependymal, well differentiated or moderately differentiated anaplastic astrocytoma; anaplastic astrocytoma; glioblastoma multiforme; ependymal tumors such as myxopapillary and well-differentiated ependymoma, anaplastic ependymoma, ependymoblastoma; oligodendroglial tumors including well-differentiated oligodendroglioma and anaplastic oligodendroglioma; mixed tumors such as mixed astrocytoma-ependymoma, mixed astrocytoma-oligodendroglioma, mixed astrocytomaependymoma-oligodendroglioma; medulloblastoma. In some embodiments the CNS malignancy is glioblastoma multiforme. In some embodiments the CNS malignancy is a secondary CNS lymphoma. In some embodiments the secondary CNS lymphoma originates from lung cancer, breast cancer, malignant melanoma, or kidney cancer.

In some embodiments the Btk inhibitor is (R)-1-(3-(4-amino-3-(4-phenoxyphenyl)-1H-pyrazolo[3,4-d]pyrimidin-1-yl)piperidin-1-yl)prop-2-en-1-one.

In some embodiments a second anti-cancer agent is administered.

In one embodiment is a method of administrating a Btk inhibitor as defined to an individual diagnosed with or suffering from a CNS malignancy with the expectation that it will result in a reduction in the severity of the malignancy, or delay the progression of the malignancy.

In another embodiment, is a method of treating a primary cancer, neoplasm or tumor of the brain or related tissues that grows in an uncontrolled manner, possibly invading nearby tissue and/or metastasizing (spreading) to other sites via the bloodstream. In a further embodiment, is a method for treating a glioma which in some instances refers to tumors that begin in the glial (supportive) tissue of the CNS. In a further embodiment, the gliomas include astrocytomas, ependymomas, oligodendrogliomas, and tumors with mixtures of two or more of these cell types. In another embodiment is a method for treating CNS malignancies selected from: astrocytic tumors such as juvenile pilocytic, subependymal, well differentiated or moderately differentiated anaplastic astrocytoma; anaplastic astrocytoma; glioblastoma multiforme; ependymal tumors such as myxopapillary and well-differentiated ependymoma, anaplastic ependymoma, ependymoblastoma; oligodendroglial tumors including well-differentiated oligodendroglioma and anaplastic oligodendroglioma; mixed tumors such as mixed astrocytoma-ependymoma, mixed astrocytoma-oligodendroglioma, mixed astrocytomaependymoma-oligodendroglioma; medulloblastoma; and any other infiltrating or non-infiltrating CNS tumors or cancers.

Described herein, in certain embodiments, are methods for treating a disorder characterized by the presence or development of one or more CNS malignancies comprising administering to an individual in need thereof a kinase inhibitor that selectively and irreversibly binds to a protein tyrosine kinase selected from Btk, a Btk homolog, a Btk kinase cysteine homolog, an ACK, and HER4, in which the kinase inhibitor reversibly and non-selectively binds to a multiplicity of protein tyrosine kinases, and further in which the plasma half life of the kinase inhibitor is less than about 4 hours. In some embodiments, the kinase inhibitor selectively and irreversibly binds to at least one of Btk, Jak3, Blk, Bmx, Tec, HER4, and Itk. In some embodiments, the kinase inhibitor selectively and irreversibly binds to Btk.

In some embodiments, the kinase inhibitor has the structure of Formula (VII):

wherein:

-   -   is a moiety that binds to the active site of a kinase, including         a tyrosine kinase, further including a Btk kinase cysteine         homolog;     -   Y is an optionally substituted group selected from among         alkylene, heteroalkylene, arylene, heteroarylene,         heterocycloalkylene, cycloalkylene, alkylenearylene,         alkyleneheteroarylene, alkylenecycloalkylene, and         alkyleneheterocycloalkylene;     -   Z is C(═O), OC(═O), NHC(═O), NCH₃C(═O), C(═S), S(═O)_(x),         OS(═O)_(x), NHS(═O)_(x), where x is 1 or 2;     -   R₇ and R₈ are independently selected from among H, unsubstituted         C₁-C₄ alkyl, substituted C₁-C₄alkyl, unsubstituted         C₁-C₄heteroalkyl, substituted C₁-C₄heteroalkyl, unsubstituted         C₃-C₆cycloalkyl, substituted C₃-C₆cycloalkyl, unsubstituted         C₂-C₆heterocycloalkyl, and substituted C₂-C₆heterocycloalkyl; or     -   R₇ and R₈ taken together form a bond;     -   R₆ is H, substituted or unsubstituted C₁-C₄alkyl, substituted or         unsubstituted C₁-C₄heteroalkyl, C₁-C₆alkoxyalkyl,         C₁-C₈alkylaminoalkyl, C₁-C₈hydroxyalkylaminoalkyl, substituted         or unsubstituted C₃-C₆cycloalkyl, substituted or unsubstituted         aryl, substituted or unsubstituted C₂-C₈heterocycloalkyl,         substituted or unsubstituted heteroaryl, C₁-C₄alkyl(aryl),         C₁-C₄alkyl(heteroaryl), C₁-C₄alkyl(C₃-C₈cycloalkyl), or         C₁-C₄alkyl(C₂-C₈heterocycloalkyl); and     -   pharmaceutically active metabolites, or pharmaceutically         acceptable solvates, pharmaceutically acceptable salts, or         pharmaceutically acceptable prodrugs thereof.

In some embodiments,

is a substituted fused biaryl moiety selected from

In some embodiments, Z is C(═O), NHC(═O), NCH₃C(═O), or S(═O)₂. In some embodiments, each of R₇ and R₈ is H; or R₇ and R₈ taken together form a bond. In some embodiments, R₆ is H, substituted or unsubstituted C₁-C₄alkyl, substituted or unsubstituted C₁-C₄heteroalkyl, C₁-C₆alkoxyalkyl, C₁-C₈alkylaminoalkyl, C₁-C₈hydroxyalkylaminoalkyl, C₁-C₈alkoxyalkylaminoalkyl, C₁-C₄alkyl(aryl), C₁-C₄alkyl(heteroaryl), C₁-C₄alkyl(C₃-C₈cycloalkyl), or C₁-C₄alkyl(C₂-C₈heterocycloalkyl). In some embodiments, Y is a 4-, 5-, 6-, or 7-membered cycloalkylene ring; or Y is a 4-, 5-, 6-, or 7-membered heterocycloalkylene ring; or Y is a C₁-C₄ alkylene, or 4-, 5-, 6-, or 7-membered heterocycloalkylene ring.

In further embodiments, the disorder is characterized by the presence or development of one or more CNS tumors. In another embodiment, the CNS tumor is classified as gliomas or nongliomas. In some embodiments, the cancer is a nonglioma. In other embodiments, the nongliomas include meningiomas, pituitary adenomas, primary CNS lymphomas, and medulloblastomas.

In some embodiments, the cancer is a brain cancer. In some embodiments, the brain cancer is a glioblastoma. In yet another embodiment, the gliomas include astrocytomas, oligodendrogliomas (or mixtures of oligodendroglioma and astocytoma elements), and ependymomas. In some embodiments, the cancer is an astrocytoma. Astrocytomas include, but are not limited to, low-grade astrocytomas, anaplastic astrocytomas, glioblastoma multiforme, pilocytic astrocytoma, pleomorphic xanthoastrocytoma, and subependymal giant cell astrocytoma. Glioblastoma multiforme is the most common and most malignant of the primary brain tumors.

In some embodiments, the cancer is an oligodendroglioma. Oligodendrogliomas include low-grade oligodendrogliomas (or oligoastrocytomas) and anaplastic oligodendriogliomas.

In some embodiments, the disorder characterized by the presence or development of one or more tumors associated with neurofibroma, optic glioma, malignant peripheral nerve sheath tumor, schwannoma, ependymoma, or meningioma.

Compounds described herein include those that have a structure of any of Formula (A1-A6), Formula (B1-B6), Formula (C1-C6), Formula (D1-D6), Formula (I), or Formula (VII), and pharmaceutically acceptable salts, solvates, esters, acids and prodrugs thereof. In certain embodiments, isomers and chemically protected forms of compounds having a structure represented by any of Formula (A1-A6), Formula (B1-B6), Formula (C1-C6), Formula (D1-D6), Formula (I), or Formula (VII), are also provided.

In one aspect, provided herein are compounds of Formula (I). Formula (I) is as follows:

wherein

-   -   L_(a) is CH₂, O, NH or S;     -   Ar is a substituted or unsubstituted aryl, or a substituted or         unsubstituted heteroaryl; and either     -   (a) Y is an optionally substituted group selected from among         alkylene, heteroalkylene, arylene, heteroarylene,         alkylenearylene, alkyleneheteroarylene, alkylenecycloalkylene         and alkyleneheterocycloalkylene;     -   Z is C(═O), NHC(═O), NR^(a)C(═O), NR^(a)S(═O)_(x), where x is 1         or 2, and R^(a) is H, substituted or unsubstituted alkyl,         substituted or unsubstituted cycloalkyl; and either     -   (i) R₇ and R₈ are H;     -   R₆ is H, substituted or unsubstituted C₁-C₄alkyl, substituted or         unsubstituted C₁-C₄heteroalkyl, C₁-C₈alkylaminoalkyl, C₁-C₈         hydroxyalkylaminoalkyl, C₁-C₈ alkoxyalkylaminoalkyl, substituted         or unsubstituted C₃-C₆cycloalkyl, substituted or unsubstituted         C₁-C₈alkylC₃-C₆cycloalkyl, substituted or unsubstituted aryl,         substituted or unsubstituted C₂-C₈heterocycloalkyl, substituted         or unsubstituted heteroaryl, C₁-C₄alkyl(aryl),         C₁-C₄alkyl(heteroaryl), C₁-C₈alkylethers, C₁-C₈alkylamides, or         C₁-C₄alkyl(C₂-C₈heterocycloalkyl);     -   (ii) R₆ and R₈ are H;     -   R₇ is H, substituted or unsubstituted C₁-C₄alkyl, substituted or         unsubstituted C₁-C₄heteroalkyl, C₁-C₈alkylaminoalkyl, C₁-C₈         hydroxyalkylaminoalkyl, C₁-C₈ alkoxyalkylaminoalkyl, substituted         or unsubstituted C₃-C₆cycloalkyl, substituted or unsubstituted         C₁-C₈alkylC₃-C₆cycloalkyl, substituted or unsubstituted aryl,         substituted or unsubstituted C₂-C₈heterocycloalkyl, substituted         or unsubstituted heteroaryl, C₁-C₄alkyl(aryl),         C₁-C₄alkyl(heteroaryl), C₁-C₈alkylethers, C₁-C₈alkylamides, or         C₁-C₄alkyl(C₂-C₈heterocycloalkyl); or     -   (iii) R₇ and R₈ taken together form a bond;     -   R₆ is H, substituted or unsubstituted C₁-C₄alkyl, substituted or         unsubstituted C₁-C₄heteroalkyl, C₁-C₈alkylaminoalkyl, C₁-C₈         hydroxyalkylaminoalkyl, C₁-C₈ alkoxyalkylaminoalkyl, substituted         or unsubstituted C₃-C₆cycloalkyl, substituted or unsubstituted         C₁-C₈alkylC₃-C₆cycloalkyl, substituted or unsubstituted aryl,         substituted or unsubstituted C₂-C₈heterocycloalkyl, substituted         or unsubstituted heteroaryl, C₁-C₄alkyl(aryl),         C₁-C₄alkyl(heteroaryl), C₁-C₈alkylethers, C₁-C₈alkylamides, or         C₁-C₄alkyl(C₂-C₈heterocycloalkyl); or     -   (b) Y is an optionally substituted group selected from         cycloalkylene or heterocycloalkylene; Z is C(═O), NHC(═O),         NR^(a)C(═O), NR^(a)S(═O)_(x), where x is 1 or 2, and R^(a) is H,         substituted or unsubstituted alkyl, substituted or unsubstituted         cycloalkyl; and either     -   (i) R₇ and R₈ are H;     -   R₆ is substituted or unsubstituted C₁-C₄heteroalkyl, C₁-C₈         hydroxyalkylaminoalkyl, C₁-C₈ alkoxyalkylaminoalkyl, substituted         or unsubstituted C₃-C₆cycloalkyl, substituted or unsubstituted         C₁-C₈alkylC₃-C₆cycloalkyl, substituted or unsubstituted aryl,         substituted or unsubstituted C₂-C₈heterocycloalkyl, substituted         or unsubstituted heteroaryl, C₁-C₄alkyl(aryl),         C₁-C₄alkyl(heteroaryl), C₁-C₈alkylethers, C₁-C₈alkylamides, or         C₁-C₄alkyl(C₂-C₈heterocycloalkyl);     -   (ii) R₆ and R₈ are H;     -   R₇ is substituted or unsubstituted C₁-C₄heteroalkyl, C₁-C₈         hydroxyalkylaminoalkyl, C₁-C₈ alkoxyalkylaminoalkyl, substituted         or unsubstituted C₃-C₆cycloalkyl, substituted or unsubstituted         C₁-C₈alkylC₃-C₆cycloalkyl, substituted or unsubstituted aryl,         substituted or unsubstituted C₂-C₈heterocycloalkyl, substituted         or unsubstituted heteroaryl, C₁-C₄alkyl(aryl),         C₁-C₄alkyl(heteroaryl), C₁-C₈alkylethers, C₁-C₈alkylamides, or         C₁-C₄alkyl(C₂-C₈heterocycloalkyl); or     -   (iii) R₇ and R₈ taken together form a bond;     -   R₆ is substituted or unsubstituted C₁-C₄alkyl, substituted or         unsubstituted C₁-C₄heteroalkyl, C₁-C₈alkylaminoalkyl,         C₁-C₈hydroxyalkylaminoalkyl, C₁-C₈alkoxyalkylaminoalkyl,         substituted or unsubstituted C₃-C₆cycloalkyl, substituted or         unsubstituted C₁-C₈alkylC₃-C₆cycloalkyl, substituted or         unsubstituted aryl, substituted or unsubstituted         C₂-C₈heterocycloalkyl, substituted or unsubstituted heteroaryl,         C₁-C₄alkyl(aryl), C₁-C₄alkyl(heteroaryl), C₁-C₈alkylethers,         C₁-C₈alkylamides, or C₁-C₄alkyl(C₂-C₈heterocycloalkyl); and         pharmaceutically active metabolites, or pharmaceutically         acceptable solvates, pharmaceutically acceptable salts, or         pharmaceutically acceptable prodrugs thereof.

In another embodiment are provided pharmaceutically acceptable salts of compounds of Formula (I). By way of example only, are salts of an amino group formed with inorganic acids such as hydrochloric acid, hydrobromic acid, phosphoric acid, sulfuric acid and perchloric acid or with organic acids such as acetic acid, oxalic acid, maleic acid, tartaric acid, citric acid, succinic acid or malonic acid. Further salts include those in which the counterion is an anion, such as adipate, alginate, ascorbate, aspartate, benzenesulfonate, benzoate, bisulfate, borate, butyrate, camphorate, camphorsulfonate, citrate, cyclopentanepropionate, digluconate, dodecylsulfate, ethanesulfonate, formate, fumarate, glucoheptonate, glycerophosphate, gluconate, hemisulfate, heptanoate, hexanoate, hydroiodide, 2-hydroxy-ethanesulfonate, lactobionate, lactate, laurate, lauryl sulfate, malate, maleate, malonate, methanesulfonate, 2-naphthalenesulfonate, nicotinate, nitrate, oleate, oxalate, palmitate, pamoate, pectinate, persulfate, 3-phenylpropionate, phosphate, picrate, pivalate, propionate, stearate, succinate, sulfate, tartrate, thiocyanate, p-toluenesulfonate, undecanoate, and valerate. Further salts include those in which the counterion is a cation, such as sodium, lithium, potassium, calcium, magnesium, ammonium, and quaternary ammonium (substituted with at least one organic moiety) cations.

In another embodiment are pharmaceutically acceptable esters of compounds of Formula (I), including those in which the ester group is selected from a formate, acetate, propionate, butyrate, acrylate and ethylsuccinate.

In another embodiment are pharmaceutically acceptable carbamates of compounds of Formula (I). In another embodiment are pharmaceutically acceptable N-acyl derivatives of compounds of Formula (I). Examples of N-acyl groups include N-acetyl and N-ethoxycarbonyl groups.

For any and all of the embodiments, substituents are optionally selected from among from a subset of the listed alternatives. For example, in some embodiments, L_(a) is CH₂, O, or NH. In other embodiments, L_(a) is O or NH. In yet other embodiments, L_(a) is O.

In some embodiments, Ar is a substituted or unsubstituted aryl. In yet other embodiments, Ar is a 6-membered aryl. In some other embodiments, Ar is phenyl.

In some embodiments, x is 2. In yet other embodiments, Z is C(═O), OC(═O), NHC(═O), S(═O)_(x), OS(═O)_(x), or NHS(═O)_(x). In some other embodiments, Z is C(═O), NHC(═O), or NCH₃C(═O).

In some embodiments Y is an optionally substituted group selected from among alkylene, heteroalkylene, arylene, heteroarylene, alkylenearylene, alkyleneheteroarylene, and alkyleneheterocycloalkylene.

In some embodiments, Z is C(═O), NHC(═O), NR^(a)C(═O), NR^(a)S(═O)_(x), where x is 1 or 2, and R^(a) is H, substituted or unsubstituted alkyl, substituted or unsubstituted cycloalkyl.

In some embodiments, R₇ and R₈ are H; and R₆ is H, substituted or unsubstituted C₁-C₄alkyl, substituted or unsubstituted C₁-C₄heteroalkyl, C₁-C₈alkylaminoalkyl, C₁-C₈hydroxyalkylaminoalkyl, C₁-C₈alkoxyalkylaminoalkyl, substituted or unsubstituted C₃-C₆cycloalkyl, substituted or unsubstituted C₁-C₈alkylC₃-C₆cycloalkyl, substituted or unsubstituted aryl, substituted or unsubstituted C₂-C₈heterocycloalkyl, substituted or unsubstituted heteroaryl, C₁-C₄alkyl(aryl), C₁-C₄alkyl(heteroaryl), C₁-C₈alkylethers, C₁-C₈alkylamides, or C₁-C₄alkyl(C₂-C₈heterocycloalkyl). In other embodiments, R₆ and R₈ are H; and R₇ is H, substituted or unsubstituted C₁-C₄alkyl, substituted or unsubstituted C₁-C₄heteroalkyl, C₁-C₈alkylaminoalkyl, C₁-C₈hydroxyalkylaminoalkyl, C₁-C₈alkoxyalkylaminoalkyl, substituted or unsubstituted C₃-C₆cycloalkyl, substituted or unsubstituted C₁-C₈alkylC₃-C₆cycloalkyl, substituted or unsubstituted aryl, substituted or unsubstituted C₂-C₈heterocycloalkyl, substituted or unsubstituted heteroaryl, C₁-C₄alkyl(aryl), C₁-C₄alkyl(heteroaryl), C₁-C₈alkylethers, C₁-C₈alkylamides, or C₁-C₄alkyl(C₂-C₈heterocycloalkyl). In yet further embodiments, R₇ and R₈ taken together form a bond; and R₆ is H, substituted or unsubstituted C₁-C₄alkyl, substituted or unsubstituted C₁-C₄heteroalkyl, C₁-C₈alkylaminoalkyl, C₁-C₈hydroxyalkylaminoalkyl, C₁-C₈alkoxyalkylaminoalkyl, substituted or unsubstituted C₃-C₆cycloalkyl, substituted or unsubstituted C₁-C₈alkylC₃-C₆cycloalkyl, substituted or unsubstituted aryl, substituted or unsubstituted C₂-C₈heterocycloalkyl, substituted or unsubstituted heteroaryl, C₁-C₄alkyl(aryl), C₁-C₄alkyl(heteroaryl), C₁-C₈alkylethers, C₁-C₈alkylamides, or C₁-C₄alkyl(C₂-C₈heterocycloalkyl).

In some embodiments, Y is an optionally substituted group selected from cycloalkylene or heterocycloalkylene.

In some embodiments, Z is C(═O), NHC(═O), NR^(a)C(═O), NR^(a)S(═O)_(x), where x is 1 or 2, and R^(a) is H, substituted or unsubstituted alkyl, substituted or unsubstituted cycloalkyl.

In some embodiments, R₇ and R₈ are H; and R₆ is substituted or unsubstituted C₁-C₄heteroalkyl, C₁-C₈hydroxyalkylaminoalkyl, C₁-C₈alkoxyalkylaminoalkyl, substituted or unsubstituted C₃-C₆cycloalkyl, substituted or unsubstituted C₁-C₈alkylC₃-C₆cycloalkyl, substituted or unsubstituted aryl, substituted or unsubstituted C₂-C₈heterocycloalkyl, substituted or unsubstituted heteroaryl, C₁-C₄alkyl(aryl), C₁-C₄alkyl(heteroaryl), C₁-C₈alkylethers, C₁-C₈alkylamides, or C₁-C₄alkyl(C₂-C₈heterocycloalkyl). In other embodiments, R₆ and R₈ are H; and R₇ is substituted or unsubstituted C₁-C₄heteroalkyl, C₁-C₈hydroxyalkylaminoalkyl, C₁-C₈alkoxyalkylaminoalkyl, substituted or unsubstituted C₃-C₆cycloalkyl, substituted or unsubstituted C₁-C₈alkylC₃-C₆cycloalkyl, substituted or unsubstituted aryl, substituted or unsubstituted C₂-C₈heterocycloalkyl, substituted or unsubstituted heteroaryl, C₁-C₄alkyl(aryl), C₁-C₄alkyl(heteroaryl), C₁-C₈alkylethers, C₁-C₈alkylamides, or C₁-C₄alkyl(C₂-C₈heterocycloalkyl). In further embodiments, R₇ and R₈ taken together form a bond; and R₆ is substituted or unsubstituted C₁-C₄alkyl, substituted or unsubstituted C₁-C₄heteroalkyl, C₁-C₈alkylaminoalkyl, C₁-C₈hydroxyalkylaminoalkyl, C₁-C₈alkoxyalkylaminoalkyl, substituted or unsubstituted C₃-C₆cycloalkyl, substituted or unsubstituted C₁-C₈alkylC₃-C₆cycloalkyl, substituted or unsubstituted aryl, substituted or unsubstituted C₂-C₈heterocycloalkyl, substituted or unsubstituted heteroaryl, C₁-C₄alkyl(aryl), C₁-C₄alkyl(heteroaryl), C₁-C₈alkylethers, C₁-C₈alkylamides, or C₁-C₄alkyl(C₂-C₈heterocycloalkyl).

Any combination of the groups described above for the various variables is contemplated herein.

In a further aspect are provided pharmaceutical compositions, which include a therapeutically effective amount of at least one of any of the compounds herein, or a pharmaceutically acceptable salt, pharmaceutically active metabolite, pharmaceutically acceptable prodrug, or pharmaceutically acceptable solvate. In certain embodiments, compositions provided herein further include a pharmaceutically acceptable diluent, excipient and/or binder.

Pharmaceutical compositions formulated for administration by an appropriate route and means containing effective concentrations of one or more of the compounds provided herein, or pharmaceutically effective derivatives thereof, that deliver amounts effective for the treatment, prevention, or amelioration of one or more symptoms of diseases, diseases or disorders that are modulated or otherwise affected by tyrosine kinase activity, or in which tyrosine kinase activity is implicated, are provided. The effective amounts and concentrations are effective for ameliorating any of the symptoms of any of the diseases, diseases or disorders disclosed herein.

In certain embodiments, provided herein is a pharmaceutical composition containing: i) a physiologically acceptable carrier, diluent, and/or excipient; and ii) one or more compounds provided herein.

In one aspect, provided herein are methods for treating an individual with a disease treatable by a compound disclosed herein, the method comprising administering a compound provided herein. In some embodiments, provided herein is a method of inhibiting the activity of tyrosine kinase(s) (e.g., Btk, HER4, an ACK, or a Btk tyrosine kinase cysteine homolog), or of treating a disorder, which benefits from inhibition of tyrosine kinase(s) (e.g., Btk, HER4, an ACK, or a Btk tyrosine kinase cysteine homolog), in an individual, which includes administering to the patient a therapeutically effective amount of at least one of any of the compounds herein, or pharmaceutically acceptable salt, pharmaceutically active metabolite, pharmaceutically acceptable prodrug, or pharmaceutically acceptable solvate.

In some embodiments, compounds provided herein are administered to a mammal. In some embodiments, the mammal is a human. In some embodiments, the mammal is a non-human. In some embodiments, compounds provided herein are orally administered. In other embodiments, the pharmaceutical formulation that is formulated for a route of administration is selected from oral administration, parenteral administration, buccal administration, nasal administration, topical administration, or rectal administration.

In other embodiments, compounds provided herein are used for the formulation of a medicament for the inhibition of tyrosine kinase activity. In some other embodiments, compounds provided herein are used for the formulation of a medicament for treating CNS malignancies. In a further embodiment, the CNS malignancy is a brain tumor. In yet another embodiment, the CNS malignancy is a glioma.

Articles of manufacture including packaging material, a compound or composition or pharmaceutically acceptable derivative thereof provided herein, which is effective for inhibiting the activity of tyrosine kinase(s), such as Btk, within the packaging material, and a label that indicates that the compound or composition, or pharmaceutically acceptable salt, pharmaceutically active metabolite, pharmaceutically acceptable prodrug, or pharmaceutically acceptable solvate thereof, is used for inhibiting the activity of tyrosine kinase(s) (e.g., Btk, HER4, an ACK, or a Btk tyrosine kinase cysteine homolog) are provided.

In another aspect are inhibited tyrosine kinases comprising a Bruton's tyrosine kinase, a Bruton's tyrosine kinase homolog, a Btk tyrosine kinase cysteine homolog thereof, an ACK covalently bound to an inhibitor, or HER4 covalently bound to an inhibitor having the structures:

wherein

indicates the point of attachment between the inhibitor and the tyrosine kinase. In a further embodiment, the inhibitor is covalently bound to a cysteine residue on the tyrosine kinase.

In any of the aforementioned embodiments, the irreversible inhibitors have the structure of Formula (VII):

wherein:

-   -   wherein

-   -    is a moiety that binds to the active site of a kinase,         including a tyrosine kinase, further including a Btk kinase         cysteine homolog;     -   Y is an optionally substituted group selected from among         alkylene, heteroalkylene, arylene, heteroarylene,         heterocycloalkylene, cycloalkylene, alkylenearylene,         alkyleneheteroarylene, alkylenecycloalkylene, and         alkyleneheterocycloalkylene;     -   Z is C(═O), OC(═O), NHC(═O), NCH₃C(═O), C(═S), S(═O)_(x),         OS(═O)_(x), NHS(═O)_(x), where x is 1 or 2;     -   R₇ and R₈ are independently selected from among H, unsubstituted         C₁-C₄ alkyl, substituted C₁-C₄alkyl, unsubstituted         C₁-C₄heteroalkyl, substituted C₁-C₄heteroalkyl, unsubstituted         C₃-C₆cycloalkyl, substituted C₃-C₆cycloalkyl, unsubstituted         C₂-C₆heterocycloalkyl, and substituted C₂-C₆heterocycloalkyl; or     -   R₇ and R₈ taken together form a bond;     -   R₆ is H, substituted or unsubstituted C₁-C₄alkyl, substituted or         unsubstituted C₁-C₄heteroalkyl, C₁-C₆alkoxyalkyl,         C₁-C₈alkylaminoalkyl, C₁-C₈hydroxyalkylaminoalkyl,         C₁-C₈alkoxyalkylaminoalkyl, substituted or unsubstituted         C₃-C₆cycloalkyl, substituted or unsubstituted aryl, substituted         or unsubstituted C₂-C₈heterocycloalkyl, substituted or         unsubstituted heteroaryl, C₁-C₄alkyl(aryl),         C₁-C₄alkyl(heteroaryl), C₁-C₄alkyl(C₃-C₈cycloalkyl), or         C₁-C₄alkyl(C₂-C₈heterocycloalkyl); and     -   pharmaceutically active metabolites, or pharmaceutically         acceptable solvates, pharmaceutically acceptable salts, or         pharmaceutically acceptable prodrugs thereof.

In another embodiment are provided pharmaceutically acceptable salts of compounds of Formula (VII). By way of example only, are salts of an amino group formed with inorganic acids such as hydrochloric acid, hydrobromic acid, phosphoric acid, sulfuric acid and perchloric acid or with organic acids such as acetic acid, oxalic acid, maleic acid, tartaric acid, citric acid, succinic acid or malonic acid. Further salts include those in which the counterion is an anion, such as adipate, alginate, ascorbate, aspartate, benzenesulfonate, benzoate, bisulfate, borate, butyrate, camphorate, camphorsulfonate, citrate, cyclopentanepropionate, digluconate, dodecylsulfate, ethanesulfonate, formate, fumarate, glucoheptonate, glycerophosphate, gluconate, hemisulfate, heptanoate, hexanoate, hydroiodide, 2-hydroxy-ethanesulfonate, lactobionate, lactate, laurate, lauryl sulfate, malate, maleate, malonate, methanesulfonate, 2-naphthalenesulfonate, nicotinate, nitrate, oleate, oxalate, palmitate, pamoate, pectinate, persulfate, 3-phenylpropionate, phosphate, picrate, pivalate, propionate, stearate, succinate, sulfate, tartrate, thiocyanate, p-toluenesulfonate, undecanoate, and valerate. Further salts include those in which the counterion is a cation, such as sodium, lithium, potassium, calcium, magnesium, ammonium, and quaternary ammonium (substituted with at least one organic moiety) cations.

In another embodiment are pharmaceutically acceptable esters of compounds of Formula (VII), including those in which the ester group is selected from a formate, acetate, propionate, butyrate, acrylate and ethylsuccinate.

In another embodiment are pharmaceutically acceptable carbamates of compounds of Formula (VII). In another embodiment are pharmaceutically acceptable N-acyl derivatives of compounds of Formula (VII). Examples of N-acyl groups include N-acetyl and N-ethoxycarbonyl groups.

In some embodiments,

is a substituted fused biaryl moiety selected from

In some embodiments Z is C(═O), NHC(═O), NCH₃C(═O), or S(═O)₂. In other embodiments, x is 2. In yet other embodiments, Z is C(═O), OC(═O), NHC(═O), S(═O)_(x), OS(═O)_(x), or NHS(═O)_(x). In some other embodiments, Z is C(═O), NHC(═O), or S(═O)₂.

In some embodiments, R₇ and R₈ are independently selected from among H, unsubstituted C₁-C₄ alkyl, substituted C₁-C₄alkyl, unsubstituted C₁-C₄heteroalkyl, and substituted C₁-C₄heteroalkyl; or R₇ and R₈ taken together form a bond. In yet other embodiments, each of R₇ and R₈ is H; or R₇ and R₈ taken together form a bond.

In some embodiments, R₆ is H, substituted or unsubstituted C₁-C₄alkyl, substituted or unsubstituted C₁-C₄heteroalkyl, C₁-C₆alkoxyalkyl, C₁-C₈alkylaminoalkyl, C₁-C₈hydroxyalkylaminoalkyl, C₁-C₈alkoxyalkylaminoalkyl, substituted or unsubstituted aryl, substituted or unsubstituted heteroaryl, C₁-C₄alkyl(aryl), C₁-C₄alkyl(heteroaryl), C₁-C₄alkyl(C₃-C₈cycloalkyl), or C₁-C₄alkyl(C₂-C₈heterocycloalkyl). In some other embodiments, R₆ is H, substituted or unsubstituted C₁-C₄alkyl, substituted or unsubstituted C₁-C₄heteroalkyl, C₁-C₆alkoxyalkyl, C₁-C₂alkyl-N(C₁-C₃alkyl)₂, C₁-C₄alkyl(aryl), C₁-C₄alkyl(heteroaryl), C₁-C₄alkyl(C₃-C₈cycloalkyl), or C₁-C₄alkyl(C₂-C₈heterocycloalkyl). In yet other embodiments, R₆ is H, substituted or unsubstituted C₁-C₄alkyl, —CH₂—O—(C₁-C₃alkyl), —CH₂—N(C₁-C₃alkyl)₂, C₁-C₄alkyl(phenyl), or C₁-C₄alkyl(5- or 6-membered heteroaryl). In yet other embodiments, R₆ is H, substituted or unsubstituted C₁-C₄alkyl, —CH₂—O—(C₁-C₃alkyl), —CH₂—(C₁-C₆alkylamino), C₁-C₄alkyl(phenyl), or C₁-C₄alkyl(5- or 6-membered heteroaryl). In some embodiments, R₆ is H, substituted or unsubstituted C₁-C₄alkyl, —CH₂—O—(C₁-C₃alkyl), —CH₂—N(C₁-C₃alkyl)₂, C₁-C₁alkyl(phenyl), or C₁-C₄alkyl(5- or 6-membered heteroaryl containing 1 or 2 N atoms), or C₁-C₄alkyl(5- or 6-membered heterocycloalkyl containing 1 or 2 N atoms).

In some embodiments, Y is an optionally substituted group selected from among alkylene, heteroalkylene, cycloalkylene, and heterocycloalkylene. In other embodiments, Y is an optionally substituted group selected from among C₁-C₆alkylene, C₁-C₆heteroalkylene, 4-, 5-, 6-, or 7-membered cycloalkylene, and 4-, 5-, 6-, or 7-membered heterocycloalkylene. In yet other embodiments, Y is an optionally substituted group selected from among C₁-C₆alkylene, C₁-C₆heteroalkylene, 5- or 6-membered cycloalkylene, and 5- or 6-membered heterocycloalkylene containing 1 or 2 N atoms. In some other embodiments, Y is a 5- or 6-membered cycloalkylene, or a 5- or 6-membered heterocycloalkylene containing 1 or 2 N atoms. In some embodiments, Y is a 4-, 5-, 6-, or 7-membered cycloalkylene ring; or Y is a 4-, 5-, 6-, or 7-membered heterocycloalkylene ring.

Any combination of the groups described above for the various variables is contemplated herein.

In any of the aforementioned methods, assays and systems: such methods, assays and systems comprise a multiplicity of test irreversible inhibitors, in which the test irreversible inhibitors each have the same

moiety, but differ in at least one of Y, Z, R₆, R₇, or R₈. In further embodiments, the multiplicity of test irreversible inhibitors is a panel of test irreversible inhibitors. In further embodiments, the binding of the panel of test irreversible inhibitors to at least one kinase is determined (including a panel of kinases, further including a panel of kinases selected from Btk, Btk homologs, and Btk kinase cysteine homologs). In further embodiments, the determined binding data is used to select and/or further design a selective irreversible inhibitor.

Irreversible inhibitors described herein include those that have a structure of any of Formula (A1-A6), Formula (B1-B6), Formula (C1-C6), Formula (D1-D6), Formula (I), or Formula (VII), and pharmaceutically acceptable salts, solvates, esters, acids and prodrugs thereof. In certain embodiments, isomers and chemically protected forms of compounds having a structure represented by any of Formula (A1-A6), Formula (B1-B6), Formula (C1-C6), Formula (D1-D6), Formula (I), or Formula (VII), are also provided.

Further described herein are pharmaceutical formulations comprising the kinase inhibitors of any kinase inhibitor compound previously listed. In one embodiment the pharmaceutical formulation includes a pharmaceutical acceptable excipient. In some embodiments, pharmaceutical formulations provided herein are administered to a human. In some embodiments, the irreversible and/or selective kinase inhibitors provided herein are orally administered. In other embodiments, the irreversible and/or selective kinase inhibitors provided herein are used for the formulation of a medicament for the inhibition of tyrosine kinase activity. In some other embodiments, the irreversible and/or selective kinase inhibitors provided herein are used for the formulation of a medicament for the inhibition of a kinase activity, including a tyrosine kinase activity, including a Btk activity, including a Btk homolog activity, including a Btk kinase cysteine homolog activity, including an ACK activity, including HER4.

In any of the aforementioned aspects are further embodiments in which administration is enteral, parenteral, or both, and wherein (a) the effective amount of the compound is systemically administered to the mammal; (b) the effective amount of the compound is administered orally to the mammal; (c) the effective amount of the compound is intravenously administered to the mammal; (d) the effective amount of the compound administered by inhalation; (e) the effective amount of the compound is administered by nasal administration; or (f) the effective amount of the compound is administered by injection to the mammal; (g) the effective amount of the compound is administered topically (dermal) to the mammal; (h) the effective amount of the compound is administered by ophthalmic administration; or (i) the effective amount of the compound is administered rectally to the mammal. In further embodiments the pharmaceutical formulation is formulated for a route of administration selected from oral administration, parenteral administration, buccal administration, nasal administration, topical administration, or rectal administration.

In any of the aforementioned aspects are further embodiments comprising single administrations of the effective amount of the pharmaceutical formulation, including further embodiments in which (i) the pharmaceutical formulations is administered once; (ii) the pharmaceutical formulations is administered to the mammal once a day; (iii) the pharmaceutical formulations is administered to the mammal multiple times over the span of one day; (iv) continually; or (v) continuously.

In any of the aforementioned aspects are further embodiments comprising multiple administrations of the effective amount of the pharmaceutical formulations, including further embodiments in which (i) the pharmaceutical formulations is administered in a single dose; (ii) the time between multiple administrations is every 6 hours; (iii) the pharmaceutical formulations is administered to the mammal every 8 hours. In further or alternative embodiments, the method comprises a drug holiday, wherein the administration of the pharmaceutical formulations is temporarily suspended or the dose of the pharmaceutical formulations being administered is temporarily reduced; at the end of the drug holiday, dosing of the pharmaceutical formulations is resumed. The length of the drug holiday varies from 2 days to 1 year.

Certain Terminology

It is to be understood that the foregoing general description and the following detailed description are exemplary and explanatory only and are not restrictive of any subject matter claimed. In this application, the use of the singular includes the plural unless specifically stated otherwise. It must be noted that, as used in the specification and the appended claims, the singular forms “a,” “an” and “the” include plural referents unless the context clearly dictates otherwise. In this application, the use of “or” means “and/or” unless stated otherwise. Furthermore, use of the term “including” as well as other forms, such as “include”, “includes,” and “included,” is not limiting.

Definition of standard chemistry terms are found in reference works, including Carey and Sundberg “ADVANCED ORGANIC CHEMISTRY 4^(TH) ED.” Vols. A (2000) and B (2001), Plenum Press, New York. Unless otherwise indicated, conventional methods of mass spectroscopy, NMR, HPLC, protein chemistry, biochemistry, recombinant DNA techniques and pharmacology, within the skill of the art are employed. Unless specific definitions are provided, the nomenclature employed in connection with, and the laboratory procedures and techniques of, analytical chemistry, synthetic organic chemistry, and medicinal and pharmaceutical chemistry described herein are those known in the art. Standard techniques are optionally used for chemical syntheses, chemical analyses, pharmaceutical preparation, formulation, and delivery, and treatment of patients. Standard techniques are optionally used for recombinant DNA, oligonucleotide synthesis, and tissue culture and transformation (e.g., electroporation, lipofection). Reactions and purification techniques are performed using documented methodologies or as described herein.

It is to be understood that the methods and compositions described herein are not limited to the particular methodology, protocols, cell lines, constructs, and reagents described herein and as such optionally vary. It is also to be understood that the terminology used herein is for the purpose of describing particular embodiments only, and is not intended to limit the scope of the methods and compositions described herein, which will be limited only by the appended claims.

Unless stated otherwise, the terms used for complex moieties (i.e., multiple chains of moieties) are to be read equivalently either from left to right or right to left. For example, the group alkylenecycloalkylene refers both to an alkylene group followed by a cycloalkylene group or as a cycloalkylene group followed by an alkylene group.

The suffix “ene” appended to a group indicates that such a group is a diradical. By way of example only, a methylene is a diradical of a methyl group, that is, it is a —CH₂— group; and an ethylene is a diradical of an ethyl group, i.e., —CH₂CH₂—.

An “alkyl” group refers to an aliphatic hydrocarbon group. The alkyl moiety includes a “saturated alkyl” group, which means that it does not contain any alkene or alkyne moieties. The alkyl moiety also includes an “unsaturated alkyl” moiety, which means that it contains at least one alkene or alkyne moiety. An “alkene” moiety refers to a group that has at least one carbon-carbon double bond, and an “alkyne” moiety refers to a group that has at least one carbon-carbon triple bond. The alkyl moiety, whether saturated or unsaturated, includes branched, straight chain, or cyclic moieties. Depending on the structure, an alkyl group includes a monoradical or a diradical (i.e., an alkylene group), and if a “lower alkyl” having 1 to 6 carbon atoms.

As used herein, C₁-C_(x) includes C₁-C₂, C₁-C₃ . . . C₁-C_(x)

The “alkyl” moiety optionally has 1 to 10 carbon atoms (whenever it appears herein, a numerical range such as “1 to 10” refers to each integer in the given range; e.g., “1 to 10 carbon atoms” means that the alkyl group is selected from a moiety having 1 carbon atom, 2 carbon atoms, 3 carbon atoms, etc., up to and including 10 carbon atoms, although the present definition also covers the occurrence of the term “alkyl” where no numerical range is designated). The alkyl group of the compounds described herein may be designated as “C₁-C₄ alkyl” or similar designations. By way of example only, “C₁-C₄ alkyl” indicates that there are one to four carbon atoms in the alkyl chain, i.e., the alkyl chain is selected from among methyl, ethyl, propyl, iso-propyl, n-butyl, iso-butyl, sec-butyl, and t-butyl. Thus C₁-C₄ alkyl includes C₁-C₂ alkyl and C₁-C₃ alkyl. Alkyl groups are optionally substituted or unsubstituted. Typical alkyl groups include, but are in no way limited to, methyl, ethyl, propyl, isopropyl, butyl, isobutyl, tertiary butyl, pentyl, hexyl, ethenyl, propenyl, butenyl, cyclopropyl, cyclobutyl, cyclopentyl, cyclohexyl, and the like.

The term “alkenyl” refers to a type of alkyl group in which the first two atoms of the alkyl group form a double bond that is not part of an aromatic group. That is, an alkenyl group begins with the atoms —C(R)═C(R)—R, wherein R refers to the remaining portions of the alkenyl group, which are either the same or different. The alkenyl moiety is optionally branched, straight chain, or cyclic (in which case, it is also known as a “cycloalkenyl” group). Depending on the structure, an alkenyl group includes a monoradical or a diradical (i.e., an alkenylene group). Alkenyl groups are optionally substituted. Non-limiting examples of an alkenyl group include —CH═CH₂, —C(CH₃)═CH₂, —CH═CHCH₃, —C(CH₃)═CHCH₃. Alkenylene groups include, but are not limited to, —CH═CH—, —C(CH₃)═CH—, —CH═CHCH₂—, —CH═CHCH₂CH₂— and —C(CH₃)═CHCH₂—. Alkenyl groups optionally have 2 to 10 carbons, and if a “lower alkenyl” having 2 to 6 carbon atoms.

The term “alkynyl” refers to a type of alkyl group in which the first two atoms of the alkyl group form a triple bond. That is, an alkynyl group begins with the atoms —C≡C—R, wherein R refers to the remaining portions of the alkynyl group, which is either the same or different. The “R” portion of the alkynyl moiety may be branched, straight chain, or cyclic. Depending on the structure, an alkynyl group includes a monoradical or a diradical (i.e., an alkynylene group). Alkynyl groups are optionally substituted. Non-limiting examples of an alkynyl group include, but are not limited to, —C≡CH, —C≡CCH₃, —C≡CCH₂CH₃, —C≡C—, and —C≡CCH₂—. Alkynyl groups optionally have 2 to 10 carbons, and if a “lower alkynyl” having 2 to 6 carbon atoms.

An “alkoxy” group refers to a (alkyl)O— group, where alkyl is as defined herein.

“Hydroxyalkyl” refers to an alkyl radical, as defined herein, substituted with at least one hydroxy group. Non-limiting examples of a hydroxyalkyl include, but are not limited to, hydroxymethyl, 2-hydroxyethyl, 2-hydroxypropyl, 3-hydroxypropyl, 1-(hydroxymethyl)-2-methylpropyl, 2-hydroxybutyl, 3-hydroxybutyl, 4-hydroxybutyl, 2,3-dihydroxypropyl, 1-(hydroxymethyl)-2-hydroxyethyl, 2,3-dihydroxybutyl, 3,4-dihydroxybutyl and 2-(hydroxymethyl)-3-hydroxypropyl.

“Alkoxyalkyl” refers to an alkyl radical, as defined herein, substituted with an alkoxy group, as defined herein.

The term “alkylamine” refers to the —N(alkyl)_(x)H_(y) group, where x and y are selected from among x=1, y=1 and x=2, y=0. When x=2, the alkyl groups, taken together with the N atom to which they are attached, optionally form a cyclic ring system.

“Alkylaminoalkyl” refers to an alkyl radical, as defined herein, substituted with an alkylamine, as defined herein.

“Hydroxyalkylaminoalkyl” refers to an alkyl radical, as defined herein, substituted with an alkylamine, and alkylhydroxy, as defined herein.

“Alkoxyalkylaminoalkyl” refers to an alkyl radical, as defined herein, substituted with an alkylamine and substituted with an alkylalkoxy, as defined herein.

An “amide” is a chemical moiety with the formula —C(O)NHR or —NHC(O)R, where R is selected from among alkyl, cycloalkyl, aryl, heteroaryl (bonded through a ring carbon) and heteroalicyclic (bonded through a ring carbon). In some embodiments, an amide moiety forms a linkage between an amino acid or a peptide molecule and a compound described herein, thereby forming a prodrug. Any amine, or carboxyl side chain on the compounds described herein can be amidified. The procedures and specific groups to make such amides are found in sources such as Greene and Wuts, Protective Groups in Organic Synthesis, 3^(rd) Ed., John Wiley & Sons, New York, N. Y., 1999, which is incorporated herein by reference for this disclosure.

The term “ester” refers to a chemical moiety with formula —COOR, where R is selected from among alkyl, cycloalkyl, aryl, heteroaryl (bonded through a ring carbon) and heteroalicyclic (bonded through a ring carbon). Any hydroxy, or carboxyl side chain on the compounds described herein can be esterified. The procedures and specific groups to make such esters are found in sources such as Greene and Wuts, Protective Groups in Organic Synthesis, 3^(rd) Ed., John Wiley & Sons, New York, N. Y., 1999, which is incorporated herein by reference for this disclosure.

As used herein, the term “ring” refers to any covalently closed structure. Rings include, for example, carbocycles (e.g., aryls and cycloalkyls), heterocycles (e.g., heteroaryls and non-aromatic heterocycles), aromatics (e.g. aryls and heteroaryls), and non-aromatics (e.g., cycloalkyls and non-aromatic heterocycles). Rings can be optionally substituted. Rings can be monocyclic or polycyclic.

As used herein, the term “ring system” refers to one, or more than one ring.

The term “membered ring” can embrace any cyclic structure. The term “membered” is meant to denote the number of skeletal atoms that constitute the ring. Thus, for example, cyclohexyl, pyridine, pyran and thiopyran are 6-membered rings and cyclopentyl, pyrrole, furan, and thiophene are 5-membered rings.

The term “fused” refers to structures in which two or more rings share one or more bonds.

The term “carbocyclic” or “carbocycle” refers to a ring wherein each of the atoms forming the ring is a carbon atom. Carbocycle includes aryl and cycloalkyl. The term thus distinguishes carbocycle from heterocycle (“heterocyclic”) in which the ring backbone contains at least one atom which is different from carbon (i.e. a heteroatom). Heterocycle includes heteroaryl and heterocycloalkyl. Carbocycles and heterocycles can be optionally substituted.

The term “aromatic” refers to a planar ring having a delocalized π-electron system containing 4n+2π electrons, where n is an integer. Aromatic rings can be formed from five, six, seven, eight, nine, or more than nine atoms. Aromatics can be optionally substituted. The term “aromatic” includes both carbocyclic aryl (e.g., phenyl) and heterocyclic aryl (or “heteroaryl” or “heteroaromatic”) groups (e.g., pyridine). The term includes monocyclic or fused-ring polycyclic (i.e., rings which share adjacent pairs of carbon atoms) groups.

As used herein, the term “aryl” refers to an aromatic ring wherein each of the atoms forming the ring is a carbon atom. Aryl rings can be formed by five, six, seven, eight, nine, or more than nine carbon atoms. Aryl groups can be optionally substituted. Examples of aryl groups include, but are not limited to phenyl, naphthalenyl, phenanthrenyl, anthracenyl, fluorenyl, and indenyl. Depending on the structure, an aryl group can be a monoradical or a diradical (i.e., an arylene group).

An “aryloxy” group refers to an (aryl)O— group, where aryl is as defined herein.

The term “carbonyl” as used herein refers to a group containing a moiety selected from the group consisting of —C(O)—, —S(O)—, —S(O)2-, and —C(S)—, including, but not limited to, groups containing a least one ketone group, and/or at least one aldehyde group, and/or at least one ester group, and/or at least one carboxylic acid group, and/or at least one thioester group. Such carbonyl groups include ketones, aldehydes, carboxylic acids, esters, and thioesters. In some embodiments, such groups are a part of linear, branched, or cyclic molecules.

The term “cycloalkyl” refers to a monocyclic or polycyclic radical that contains only carbon and hydrogen, and is optionally saturated, partially unsaturated, or fully unsaturated. Cycloalkyl groups include groups having from 3 to 10 ring atoms. Illustrative examples of cycloalkyl groups include the following moieties:

and the like. Depending on the structure, a cycloalkyl group is either a monoradical or a diradical (e.g., an cycloalkylene group), and if a “lower cycloalkyl” having 3 to 8 carbon atoms.

“Cycloalkylalkyl” means an alkyl radical, as defined herein, substituted with a cycloalkyl group. Non-limiting cycloalkylalkyl groups include cyclopropylmethyl, cyclobutylmethyl, cyclopentylmethyl, cyclohexylmethyl, and the like.

The term “heterocycle” refers to heteroaromatic and heteroalicyclic groups containing one to four heteroatoms each selected from O, S and N, wherein each heterocyclic group has from 4 to 10 atoms in its ring system, and with the proviso that the ring of said group does not contain two adjacent O or S atoms. Herein, whenever the number of carbon atoms in a heterocycle is indicated (e.g., C₁-C₆ heterocycle), at least one other atom (the heteroatom) must be present in the ring. Designations such as “C₁-C₆ heterocycle” refer only to the number of carbon atoms in the ring and do not refer to the total number of atoms in the ring. It is understood that the heterocylic ring can have additional heteroatoms in the ring. Designations such as “4-6 membered heterocycle” refer to the total number of atoms that are contained in the ring (i.e., a four, five, or six membered ring, in which at least one atom is a carbon atom, at least one atom is a heteroatom and the remaining two to four atoms are either carbon atoms or heteroatoms). In heterocycles that have two or more heteroatoms, those two or more heteroatoms can be the same or different from one another. Heterocycles can be optionally substituted. Binding to a heterocycle can be at a heteroatom or via a carbon atom. Non-aromatic heterocyclic groups include groups having only 4 atoms in their ring system, but aromatic heterocyclic groups must have at least 5 atoms in their ring system. The heterocyclic groups include benzo-fused ring systems. An example of a 4-membered heterocyclic group is azetidinyl (derived from azetidine). An example of a 5-membered heterocyclic group is thiazolyl. An example of a 6-membered heterocyclic group is pyridyl, and an example of a 10-membered heterocyclic group is quinolinyl. Examples of non-aromatic heterocyclic groups are pyrrolidinyl, tetrahydrofuranyl, dihydrofuranyl, tetrahydrothienyl, tetrahydropyranyl, dihydropyranyl, tetrahydrothiopyranyl, piperidino, morpholino, thiomorpholino, thioxanyl, piperazinyl, azetidinyl, oxetanyl, thietanyl, homopiperidinyl, oxepanyl, thiepanyl, oxazepinyl, diazepinyl, thiazepinyl, 1,2,3,6-tetrahydropyridinyl, 2-pyrrolinyl, 3-pyrrolinyl, indolinyl, 2H-pyranyl, 4H-pyranyl, dioxanyl, 1,3-dioxolanyl, pyrazolinyl, dithianyl, dithiolanyl, dihydropyranyl, dihydrothienyl, dihydrofuranyl, pyrazolidinyl, imidazolinyl, imidazolidinyl, 3-azabicyclo[3.1.0]hexanyl, 3-azabicyclo[4.1.0]heptanyl, 3H-indolyl and quinolizinyl. Examples of aromatic heterocyclic groups are pyridinyl, imidazolyl, pyrimidinyl, pyrazolyl, triazolyl, pyrazinyl, tetrazolyl, furyl, thienyl, isoxazolyl, thiazolyl, oxazolyl, isothiazolyl, pyrrolyl, quinolinyl, isoquinolinyl, indolyl, benzimidazolyl, benzofuranyl, cinnolinyl, indazolyl, indolizinyl, phthalazinyl, pyridazinyl, triazinyl, isoindolyl, pteridinyl, purinyl, oxadiazolyl, thiadiazolyl, furazanyl, benzofurazanyl, benzothiophenyl, benzothiazolyl, benzoxazolyl, quinazolinyl, quinoxalinyl, naphthyridinyl, and furopyridinyl. The foregoing groups, as derived from the groups listed above, are optionally C-attached or N-attached where such is possible. For instance, a group derived from pyrrole includes pyrrol-1-yl (N-attached) or pyrrol-3-yl (C-attached). Further, a group derived from imidazole includes imidazol-1-yl or imidazol-3-yl (both N-attached) or imidazol-2-yl, imidazol-4-yl or imidazol-5-yl (all C-attached). The heterocyclic groups include benzo-fused ring systems and ring systems substituted with one or two oxo (═O) moieties such as pyrrolidin-2-one. Depending on the structure, a heterocycle group can be a monoradical or a diradical (i.e., a heterocyclene group).

The terms “heteroaryl” or, alternatively, “heteroaromatic” refers to an aromatic group that includes one or more ring heteroatoms selected from nitrogen, oxygen and sulfur. An N-containing “heteroaromatic” or “heteroaryl” moiety refers to an aromatic group in which at least one of the skeletal atoms of the ring is a nitrogen atom. Illustrative examples of heteroaryl groups include the following moieties:

and the like. Depending on the structure, a heteroaryl group can be a monoradical or a diradical (i.e., a heteroarylene group).

As used herein, the term “non-aromatic heterocycle”, “heterocycloalkyl” or “heteroalicyclic” refers to a non-aromatic ring wherein one or more atoms forming the ring is a heteroatom. A “non-aromatic heterocycle” or “heterocycloalkyl” group refers to a cycloalkyl group that includes at least one heteroatom selected from nitrogen, oxygen and sulfur. In some embodiments, the radicals are fused with an aryl or heteroaryl. Heterocycloalkyl rings can be formed by three, four, five, six, seven, eight, nine, or more than nine atoms. Heterocycloalkyl rings can be optionally substituted. In certain embodiments, non-aromatic heterocycles contain one or more carbonyl or thiocarbonyl groups such as, for example, oxo- and thio-containing groups. Examples of heterocycloalkyls include, but are not limited to, lactams, lactones, cyclic imides, cyclic thioimides, cyclic carbamates, tetrahydrothiopyran, 4H-pyran, tetrahydropyran, piperidine, 1,3-dioxin, 1,3-dioxane, 1,4-dioxin, 1,4-dioxane, piperazine, 1,3-oxathiane, 1,4-oxathiin, 1,4-oxathiane, tetrahydro-1,4-thiazine, 2H-1,2-oxazine, maleimide, succinimide, barbituric acid, thiobarbituric acid, dioxopiperazine, hydantoin, dihydrouracil, morpholine, trioxane, hexahydro-1,3,5-triazine, tetrahydrothiophene, tetrahydrofuran, pyrroline, pyrrolidine, pyrrolidone, pyrrolidione, pyrazoline, pyrazolidine, imidazoline, imidazolidine, 1,3-dioxole, 1,3-dioxolane, 1,3-dithiole, 1,3-dithiolane, isoxazoline, isoxazolidine, oxazoline, oxazolidine, oxazolidinone, thiazoline, thiazolidine, and 1,3-oxathiolane. Illustrative examples of heterocycloalkyl groups, also referred to as non-aromatic heterocycles, include:

and the like. The term heteroalicyclic also includes all ring forms of the carbohydrates, including but not limited to the monosaccharides, the disaccharides and the oligosaccharides. Depending on the structure, a heterocycloalkyl group can be a monoradical or a diradical (i.e., a heterocycloalkylene group).

The term “halo” or, alternatively, “halogen” or “halide” means fluoro, chloro, bromo and iodo.

The term “haloalkyl,” refers to alkyl structures in which at least one hydrogen is replaced with a halogen atom. In certain embodiments in which two or more hydrogen atoms are replaced with halogen atoms, the halogen atoms are all the same as one another. In other embodiments in which two or more hydrogen atoms are replaced with halogen atoms, the halogen atoms are not all the same as one another.

The term “fluoroalkyl,” as used herein, refers to alkyl group in which at least one hydrogen is replaced with a fluorine atom. Examples of fluoroalkyl groups include, but are not limited to, —CF₃, —CH₂CF₃, —CF₂CF₃, —CH₂CH₂CF₃ and the like.

As used herein, the term “heteroalkyl” refers to optionally substituted alkyl radicals in which one or more skeletal chain atoms is a heteroatom, e.g., oxygen, nitrogen, sulfur, silicon, phosphorus or combinations thereof. The heteroatom(s) are placed at any interior position of the heteroalkyl group or at the position at which the heteroalkyl group is attached to the remainder of the molecule. Examples include, but are not limited to, —CH₂—O—CH₃, —CH₂—CH₂—O—CH₃, —CH₂—NH—CH₃, —CH₂—CH₂—NH—CH₃, —CH₂—N(CH₃)—CH₃, —CH₂—CH₂—NH—CH₃, —CH₂—CH₂—N(CH₃)—CH₃, —CH₂—S—CH₂—CH₃, —CH₂—CH₂, —S(O)—CH₃, —CH₂—CH₂—S(O)₂—CH₃, —CH═CH—O—CH₃, —Si(CH₃)₃, —CH₂—CH═N—OCH₃, and —CH═CH—N(CH₃)—CH₃. In addition, in some embodiments, up to two heteroatoms are consecutive, such as, by way of example, —CH₂—NH—OCH₃ and —CH₂—O—Si(CH₃)₃.

The term “heteroatom” refers to an atom other than carbon or hydrogen. Heteroatoms are typically independently selected from among oxygen, sulfur, nitrogen, silicon and phosphorus, but are not limited to these atoms. In embodiments in which two or more heteroatoms are present, the two or more heteroatoms can all be the same as one another, or some or all of the two or more heteroatoms can each be different from the others.

The term “bond” or “single bond” refers to a chemical bond between two atoms, or two moieties when the atoms joined by the bond are considered to be part of larger substructure.

The term “moiety” refers to a specific segment or functional group of a molecule. Chemical moieties are often recognized chemical entities embedded in or appended to a molecule.

A “thioalkoxy” or “alkylthio” group refers to a —S-alkyl group.

A “SH” group is also referred to either as a thiol group or a sulfhydryl group.

The term “optionally substituted” or “substituted” means that the referenced group may be substituted with one or more additional group(s) individually and independently selected from alkyl, cycloalkyl, aryl, heteroaryl, heteroalicyclic, hydroxy, alkoxy, aryloxy, alkylthio, arylthio, alkylsulfoxide, arylsulfoxide, alkylsulfone, arylsulfone, cyano, halo, acyl, nitro, haloalkyl, fluoroalkyl, amino, including mono- and di-substituted amino groups, and the protected derivatives thereof. By way of example an optional substituents may be L_(s)R_(s), wherein each L_(s) is independently selected from a bond, —O—, —C(═O)—, —S—, —S(═O)—, —S(═O)₂—, —NH—, —NHC(O)—, —C(O)NH—, S(═O)₂NH—, —NHS(═O)₂, —OC(O)NH—, —NHC(O)O—, -(substituted or unsubstituted C₁-C₆ alkyl), or -(substituted or unsubstituted C₂-C₆ alkenyl); and each R_(s) is independently selected from H, (substituted or unsubstituted C₁-C₄alkyl), (substituted or unsubstituted C₃-C₆cycloalkyl), heteroaryl, or heteroalkyl. The protecting groups that forms the protective derivatives of the above substituents include those found in sources such as Greene and Wuts, above.

The term “Michael acceptor moiety” refers to a functional group that can participate in a Michael reaction, wherein a new covalent bond is formed between a portion of the Michael acceptor moiety and the donor moiety. The Michael acceptor moiety is an electrophile and the “donor moiety” is a nucleophile. The “G” groups presented in any of Formula (A1-A6), Formula (B1-B6), Formula (C1-C6), Formula (D1-D6), Formula (I), or Formula (VII) are non-limiting examples of Michael acceptor moieties.

The term “nucleophile” or “nucleophilic” refers to an electron rich compound, or moiety thereof. An example of a nucleophile includes, but in no way is limited to, a cysteine residue of a molecule, such as, for example Cys 481 of Btk.

The term “electrophile”, or “electrophilic” refers to an electron poor or electron deficient molecule, or moiety thereof. Examples of electrophiles include, but in no way are limited to, Michael acceptor moieties.

The term “acceptable” or “pharmaceutically acceptable”, with respect to a formulation, composition or ingredient, as used herein, means having no persistent detrimental effect on the general health of the subject being treated or does not abrogate the biological activity or properties of the compound, and is relatively nontoxic.

As used herein, the term “agonist” refers to a compound, the presence of which results in a biological activity of a protein that is the same as the biological activity resulting from the presence of a naturally occurring ligand for the protein, such as, for example, Btk.

As used herein, “ACK” and “Accessible Cysteine Kinase” are synonyms. They mean a kinase with an accessible cysteine residue. ACKS include, but are not limited to, BTK, ITK, Bmx/ETK, TEC, EFGR, HER4, HER4, LCK, BLK, C-src, FGR, Fyn, HCK, Lyn, YES, ABL, Brk, CSK, FER, JAK3, SYK. In some embodiments, the ACK is HER4.

As used herein, the term “partial agonist” refers to a compound the presence of which results in a biological activity of a protein that is of the same type as that resulting from the presence of a naturally occurring ligand for the protein, but of a lower magnitude.

As used herein, the term “antagonist” refers to a compound, the presence of which results in a decrease in the magnitude of a biological activity of a protein. In certain embodiments, the presence of an antagonist results in complete inhibition of a biological activity of a protein, such as, for example, Btk. In certain embodiments, an antagonist is an inhibitor.

As used herein, “amelioration” of the symptoms of a particular disorder by administration of a particular compound or pharmaceutical composition refers to any lessening of severity, delay in onset, slowing of progression, or shortening of duration, whether permanent or temporary, lasting or transient that can be attributed to or associated with administration of the compound or composition.

“Bioavailability” refers to the percentage of the weight of compounds disclosed herein, such as, compounds of any of Formula (A1-A6), Formula (B1-B6), Formula (C1-C6), Formula (D1-D6), Formula (I), or Formula (VII), dosed that is delivered into the general circulation of the animal or human being studied. The total exposure (AUC_((0-∞))) of a drug when administered intravenously is usually defined as 100% bioavailable (F %). “Oral bioavailability” refers to the extent to which compounds disclosed herein, such as, compounds of any of Formula (A1-A6), Formula (B1-B6), Formula (C1-C6), Formula (D1-D6), Formula (I), or Formula (VII), are absorbed into the general circulation when the pharmaceutical composition is taken orally as compared to intravenous injection.

The term “biophysical probe,” as used herein, refers to probes which detect or monitor structural changes in molecules (including biomolecules) in biological systems or in the presence of other biomolecules (e.g., ex vivo, in vivo or in vitro). In some embodiments, such molecules include, but are not limited to, proteins and the “biophysical probe” is used to detect or monitor interaction of proteins with other macromolecules. In other embodiments, examples of biophysical probes include, but are not limited to, spin-labels, fluorophores, and photoactivatable groups.

“Blood plasma concentration” refers to the concentration of compounds disclosed herein, such as, compounds of any of Formula (A1-A6), Formula (B1-B6), Formula (C1-C6), Formula (D1-D6), Formula (I), or Formula (VII), in the plasma component of blood of an individual. It is understood that the plasma concentration of compounds of any of Formula (A1-A6), Formula (B1-B6), Formula (C1-C6), Formula (D1-D6), Formula (I), or Formula (VII), may vary significantly between subjects, due to variability with respect to metabolism and/or possible interactions with other therapeutic agents. In accordance with one embodiment disclosed herein, the blood plasma concentration of the compounds of any of Formula (A1-A6), Formula (B1-B6), Formula (C1-C6), Formula (D1-D6), Formula (I), or Formula (VII), does vary from subject to subject. Likewise, values such as maximum plasma concentration (C_(max)) or time to reach maximum plasma concentration (T_(max)), or total area under the plasma concentration time curve (AUC_((0-∞))) may vary from subject to subject. Due to this variability, the amount necessary to constitute “a therapeutically effective amount” of a compound of any of Formula (A1-A6), Formula (B1-B6), Formula (C1-C6), Formula (D1-D6), Formula (I), or Formula (VII), is expected to vary from subject to subject.

The term “Bruton's tyrosine kinase,” as used herein, refers to Bruton's tyrosine kinase from Homo sapiens, as disclosed in, e.g., U.S. Pat. No. 6,326,469 (GenBank Accession No. NP_(—)000052).

The term “Bruton's tyrosine kinase homolog,” as used herein, refers to orthologs of Bruton's tyrosine kinase, e.g., the orthologs from mouse (GenBank Accession No. AAB47246), dog (GenBank Accession No. XP_(—)549139.), rat (GenBank Accession No. NP_(—)001007799), chicken (GenBank Accession No. NP_(—)989564), or zebra fish (GenBank Accession No. XP_(—)698117), and fusion proteins of any of the foregoing that exhibit kinase activity towards one or more substrates of Bruton's tyrosine kinase (e.g. a peptide substrate having the amino acid sequence “AVLESEEELYSSARQ”).

The term “HER4”, also known as ERBB4, also known as “V-erb-a erythroblastic leukemia viral oncogene homolog 4” means either (a) the nucleic acid sequence encoding a receptor tyrosine kinase that is a member of the epidermal growth factor receptor subfamily, or (b) the protein thereof. For the nucleic acid sequence that comprises the human HER4 gene see GenBank Accession No. NM_(—)001042599. For the amino acid sequence that comprises the human HER4 protein see GenBank Accession No. NP_(—)001036064.

The phrase “treating a CNS malignancy” refers to administration of a compound disclosed herein to an individual diagnosed with or suffering from a CNS malignancy with the expectation that it will result in a reduction in the severity of the malignancy, or delay the progression of the malignancy. Further, it will be appreciated that not all patients respond equally to therapeutics, and therefore an actual response from every patient, or from a given individual patient is not required for treatment to have occurred.

“CNS malignancy” refers to a primary cancer, neoplasm or tumor of the brain or related tissues that grows in an uncontrolled manner, possibly invading nearby tissue and/or metastasizing (spreading) to other sites via the bloodstream. Gliomas refer to tumors that begin in the glial (supportive) tissue of the CNS. The most common gliomas include astrocytomas, ependymomas, oligodendrogliomas, and tumors with mixtures of two or more of these cell types. CNS malignancy may be used interchangeably with “tumor”, or “brain cancer.” Specific CNS malignancies suitable for treatment using the compositions and methods of the invention include, but are not limited to: astrocytic tumors such as juvenile pilocytic, subependymal, well differentiated or moderately differentiated anaplastic astrocytoma; anaplastic astrocytoma; glioblastoma multiforme; ependymal tumors such as myxopapillary and well-differentiated ependymoma, anaplastic ependymoma, ependymoblastoma; oligodendroglial tumors including well-differentiated oligodendroglioma and anaplastic oligodendroglioma; mixed tumors such as mixed astrocytoma-ependymoma, mixed astrocytoma-oligodendroglioma, mixed astrocytomaependymoma-oligodendroglioma; medulloblastoma; and any other infiltrating or non-infiltrating CNS tumors or cancers. CNS malignancies also refer to Secondary CNS lymphomas.

The terms “co-administration” or the like, as used herein, are meant to encompass administration of the selected therapeutic agents to a single patient, and are intended to include treatment regimens in which the agents are administered by the same or different route of administration or at the same or different time.

The terms “effective amount” or “therapeutically effective amount,” as used herein, refer to a sufficient amount of an agent or a compound being administered which will relieve to some extent one or more of the symptoms of the disorder being treated. The result can be reduction and/or alleviation of the signs, symptoms, or causes of a disease, or any other desired alteration of a biological system. For example, an “effective amount” for therapeutic uses is the amount of the composition including a compound as disclosed herein required to provide a clinically significant decrease in disease symptoms without undue adverse side effects. An appropriate “effective amount” in any individual case is optionally determined using techniques, such as a dose escalation study. The term “therapeutically effective amount” includes, for example, a prophylactically effective amount. An “effective amount” of a compound disclosed herein is an amount effective to achieve a desired pharmacologic effect or therapeutic improvement without undue adverse side effects. It is understood that “an effect amount” or “a therapeutically effective amount” can vary from subject to subject, due to variation in metabolism of the compound of any of Formula (A1-A6), Formula (B1-B6), Formula (C1-C6), Formula (D1-D6), Formula (I), or Formula (VII), age, weight, general condition of the subject, the condition being treated, the severity of the condition being treated, and the judgment of the prescribing physician.

The terms “enhance” or “enhancing” means to increase or prolong either in potency or duration a desired effect. By way of example, “enhancing” the effect of therapeutic agents refers to the ability to increase or prolong, either in potency or duration, the effect of therapeutic agents on during treatment of a disorder. An “enhancing-effective amount,” as used herein, refers to an amount adequate to enhance the effect of a therapeutic agent in the treatment of a disorder. When used in an individual, amounts effective for this use will depend on the severity and course of the disorder, previous therapy, the individual's health status and response to the drugs, and the judgment of the treating physician.

The term “homologous cysteine,” as used herein refers to a cysteine residue found with in a sequence position that is homologous to that of cysteine 481 of Bruton's tyrosine kinase, as defined herein. For example, cysteine 482 is the homologous cysteine of the rat ortholog of Bruton's tyrosine kinase; cysteine 479 is the homologous cysteine of the chicken ortholog; and cysteine 481 is the homologous cysteine in the zebra fish ortholog. In another example, the homologous cysteine of TXK, a Tec kinase family member related to Bruton's tyrosine, is Cys 350. Other examples of kinases having homologous cysteines are shown in FIG. 7. See also the sequence alignments of tyrosine kinases (TK) published on the world wide web at kinase.com/human/kinome/phylogeny.html.

The term “identical,” as used herein, refers to two or more sequences or subsequences which are the same. In addition, the term “substantially identical,” as used herein, refers to two or more sequences which have a percentage of sequential units which are the same when compared and aligned for maximum correspondence over a comparison window, or designated region as measured using comparison algorithms or by manual alignment and visual inspection. By way of example only, two or more sequences are “substantially identical” if the sequential units are about 60% identical, about 65% identical, about 70% identical, about 75% identical, about 80% identical, about 85% identical, about 90% identical, or about 95% identical over a specified region. Such percentages to describe the “percent identity” of two or more sequences. The identity of a sequence can exist over a region that is at least about 75-100 sequential units in length, over a region that is about 50 sequential units in length, or, where not specified, across the entire sequence. This definition also refers to the complement of a test sequence. By way of example only, two or more polypeptide sequences are identical when the amino acid residues are the same, while two or more polypeptide sequences are “substantially identical” if the amino acid residues are about 60% identical, about 65% identical, about 70% identical, about 75% identical, about 80% identical, about 85% identical, about 90% identical, or about 95% identical over a specified region. The identity can exist over a region that is at least about 75-100 amino acids in length, over a region that is about 50 amino acids in length, or, where not specified, across the entire sequence of a polypeptide sequence. In addition, by way of example only, two or more polynucleotide sequences are identical when the nucleic acid residues are the same, while two or more polynucleotide sequences are “substantially identical” if the nucleic acid residues are about 60% identical, about 65% identical, about 70% identical, about 75% identical, about 80% identical, about 85% identical, about 90% identical, or about 95% identical over a specified region. The identity can exist over a region that is at least about 75-100 nucleic acids in length, over a region that is about 50 nucleic acids in length, or, where not specified, across the entire sequence of a polynucleotide sequence.

The terms “inhibits”, “inhibiting”, or “inhibitor” of a kinase, as used herein, refer to inhibition of enzymatic phosphotransferase activity.

The term “irreversible inhibitor,” as used herein, refers to a compound that, upon contact with a target protein (e.g., a kinase) causes the formation of a new covalent bond with or within the protein, whereby one or more of the target protein's biological activities (e.g., phosphotransferase activity) is diminished or abolished notwithstanding the subsequent presence or absence of the irreversible inhibitor.

The term “irreversible Btk inhibitor,” as used herein, refers to an inhibitor of Btk that can form a covalent bond with an amino acid residue of Btk. In one embodiment, the irreversible inhibitor of Btk can form a covalent bond with a Cys residue of Btk; in particular embodiments, the irreversible inhibitor can form a covalent bond with a Cys 481 residue (or a homolog thereof) of Btk or a cysteine residue in the homologous corresponding position of another tyrosine kinase.

The term “isolated,” as used herein, refers to separating and removing a component of interest from at least some portion of components not of interest. Isolated substances can be in either a dry or semi-dry state, or in solution, including but not limited to an aqueous solution. The isolated component can be in a homogeneous state or the isolated component can be a part of a pharmaceutical composition that comprises additional pharmaceutically acceptable carriers and/or excipients. By way of example only, nucleic acids or proteins are “isolated” when such nucleic acids or proteins are free of at least some of the cellular components with which it is associated in the natural state, or that the nucleic acid or protein has been concentrated to a level greater than the concentration of its in vivo or in vitro production. Also, by way of example, a gene is isolated when separated from open reading frames which flank the gene and encode a protein other than the gene of interest.

The term “linkage,” as used herein to refer to bonds or a chemical moiety formed from a chemical reaction between the functional group of a linker and another molecule. In some embodiments, such bonds include, but are not limited to, covalent linkages and non-covalent bonds, while such chemical moieties include, but are not limited to, esters, carbonates, imines, phosphate esters, hydrazones, acetals, orthoesters, peptide linkages, and oligonucleotide linkages. Hydrolytically stable linkages means that the linkages are substantially stable in water and do not react with water at useful pH values, including but not limited to, under physiological conditions for an extended period of time, perhaps even indefinitely. Hydrolytically unstable or degradable linkages means that the linkages are degradable in water or in aqueous solutions, including for example, blood. In other embodiments, enzymatically unstable or degradable linkages means that the linkage is degraded by one or more enzymes. By way of example only, PEG and related polymers include degradable linkages in the polymer backbone or in the linker group between the polymer backbone and one or more of the terminal functional groups of the polymer molecule. Such degradable linkages include, but are not limited to, ester linkages formed by the reaction of PEG carboxylic acids or activated PEG carboxylic acids with alcohol groups on a biologically active agent, wherein such ester groups generally hydrolyze under physiological conditions to release the biologically active agent. Other hydrolytically degradable linkages include but are not limited to carbonate linkages; imine linkages resulted from reaction of an amine and an aldehyde; phosphate ester linkages formed by reacting an alcohol with a phosphate group; hydrazone linkages which are reaction product of a hydrazide and an aldehyde; acetal linkages that are the reaction product of an aldehyde and an alcohol; orthoester linkages that are the reaction product of a formate and an alcohol; peptide linkages formed by an amine group, including but not limited to, at an end of a polymer such as PEG, and a carboxyl group of a peptide; and oligonucleotide linkages formed by a phosphoramidite group, including but not limited to, at the end of a polymer, and a 5′ hydroxyl group of an oligonucleotide.

A “metabolite” of a compound disclosed herein is a derivative of that compound that is formed when the compound is metabolized. The term “active metabolite” refers to a biologically active derivative of a compound that is formed when the compound is metabolized. The term “metabolized,” as used herein, refers to the sum of the processes (including, but not limited to, hydrolysis reactions and reactions catalyzed by enzymes, such as, oxidation reactions) by which a particular substance is changed by an organism. Thus, enzymes produce specific structural alterations to a compound. For example, cytochrome P450 catalyzes a variety of oxidative and reductive reactions while uridine diphosphate glucuronyl transferases catalyze the transfer of an activated glucuronic-acid molecule to aromatic alcohols, aliphatic alcohols, carboxylic acids, amines and free sulfhydryl groups. Further information on metabolism is obtained from The Pharmacological Basis of Therapeutics, 9th Edition, McGraw-Hill (1996). Metabolites of the compounds disclosed herein are optionally identified either by administration of compounds to a host and analysis of tissue samples from the host, or by incubation of compounds with hepatic cells in vitro and analysis of the resulting compounds. In some embodiments, metabolites of a compound are formed by oxidative processes and correspond to the corresponding hydroxy-containing compound. In some embodiments, a compound is metabolized to pharmacologically active metabolites.

The term “modulate,” as used herein, means to interact with a target either directly or indirectly so as to alter the activity of the target, including, by way of example only, to enhance the activity of the target, to inhibit the activity of the target, to limit the activity of the target, or to extend the activity of the target.

As used herein, the term “modulator” refers to a compound that alters an activity of a molecule. For example, a modulator can cause an increase or decrease in the magnitude of a certain activity of a molecule compared to the magnitude of the activity in the absence of the modulator. In certain embodiments, a modulator is an inhibitor, which decreases the magnitude of one or more activities of a molecule. In certain embodiments, an inhibitor completely prevents one or more activities of a molecule. In certain embodiments, a modulator is an activator, which increases the magnitude of at least one activity of a molecule. In certain embodiments the presence of a modulator results in an activity that does not occur in the absence of the modulator.

The term “plasma half life,” as used herein refers to half-life in rat, dog or human as determined by measure drug concentration over time in plasma following a single dose and fitting data to standard pharmacokinetic models using software such as WinNonLin to determine the time at which drug has been 50% eliminated from plasma.

The term “prophylactically effective amount,” as used herein, refers that amount of a composition applied to an individual which will relieve to some extent one or more of the symptoms of a disease, disorder being treated. In such prophylactic applications, such amounts may depend on the patient's state of health, weight, and the like.

As used herein, the term “selective binding compound” refers to a compound that selectively binds to any portion of one or more target proteins.

As used herein, the term “selectively binds” refers to the ability of a selective binding compound to bind to a target protein, such as, for example, Btk, with greater affinity than it binds to a non-target protein. In certain embodiments, specific binding refers to binding to a target with an affinity that is at least 10, 50, 100, 250, 500, 1000 or more times greater than the affinity for a non-target.

As used herein, the term “selective modulator” refers to a compound that selectively modulates a target activity relative to a non-target activity. In certain embodiments, specific modulator refers to modulating a target activity at least 10, 50, 100, 250, 500, 1000 times more than a non-target activity.

The term “substantially purified,” as used herein, refers to a component of interest that may be substantially or essentially free of other components which normally accompany or interact with the component of interest prior to purification. By way of example only, a component of interest may be “substantially purified” when the preparation of the component of interest contains less than about 30%, less than about 25%, less than about 20%, less than about 15%, less than about 10%, less than about 5%, less than about 4%, less than about 3%, less than about 2%, or less than about 1% (by dry weight) of contaminating components. Thus, a “substantially purified” component of interest may have a purity level of about 70%, about 75%, about 80%, about 85%, about 90%, about 95%, about 96%, about 97%, about 98%, about 99% or greater.

The term “individual” as used herein, refers to a mammal which is the object of treatment, observation or experiment. The term is not to be construed as requiring the supervision of a medical practicioner (e.g., a physician, physician's assistant, nurse, orderly, hospice care worker).

As used herein, the term “target activity” refers to a biological activity capable of being modulated by a selective modulator. Certain exemplary target activities include, but are not limited to, binding affinity, signal transduction, enzymatic activity, tumor growth, inflammation or inflammation-related processes, and amelioration of one or more symptoms associated with a disorder.

As used herein, the term “target protein” refers to a molecule or a portion of a protein capable of being bound by a selective binding compound. In certain embodiments, a target protein is Btk.

The terms “treat,” “treating” or “treatment”, as used herein, include alleviating, abating or ameliorating a symptom of a disorder, preventing additional symptoms, ameliorating or preventing the underlying metabolic causes of symptoms, inhibiting the disorder, e.g., arresting the development of the disorder, relieving the disorder, causing regression of the disorder, relieving a condition caused by the disorder, or stopping the symptoms of the disorder. The terms “treat,” “treating” or “treatment”, include, but are not limited to, prophylactic and/or therapeutic treatments.

As used herein, the IC₅₀ refers to an amount, concentration or dosage of a particular test compound that achieves a 50% inhibition of a maximal response, such as inhibition of Btk, in an assay that measures such response.

As used herein, EC₅₀ refers to a dosage, concentration or amount of a particular test compound that elicits a dose-dependent response at 50% of maximal expression of a particular response that is induced, provoked or potentiated by the particular test compound.

FIGURES

FIG. 1A-FIG. 1D illustrates the structures of PCI-32765, PCI-45227, PCI-32765-d5 (IS), and PCI-45227-d5 (IS).

FIG. 2 illustrates representative Chromatogram of Blank CSF.

FIG. 3 illustrates representative Chromatogram of Lowest Standard for PCI-32765.

FIG. 4 illustrates representative Chromatogram of Lowest Standard for PCI-45227.

FIG. 5 illustrates representative Chromatogram of Mid-QC for PCI-32765.

FIG. 6 illustrates representative Chromatogram of Mid-QC for PCI-45227.

FIG. 7 illustrates representative Standard Calibration Curve for PCI-32765.

FIG. 8 illustrates representative Standard Calibration Curve for PCI-45227.

FIG. 9 illustrates representative Calibration Curve for PCI-32765 in human CSF.

FIG. 10 illustrates representative Calibration Curve for PCI-45227 in human CSF.

FIG. 11 illustrates representative Calibration Curve for PCI-32765 in human plasma.

FIG. 12 illustrates representative Calibration Curve for PCI-45227 in human plasma.

FIG. 13 illustrates CSF and plasma concentration ratios for PCI-32765 and PCI-45227.

DETAILED DESCRIPTION OF THE INVENTION CNS Malignancies

In some embodiments, the compounds and formulations described herein are utilized to treat one or more disorders characterized by the presence or development of a CNS malignancy. In one embodiment, the CNS malignancy is a CNS lymphoma. In a further embodiment, the CNS malignancy is a glioma. Glioma types include but are not limited to, astrocytic tumors including astrocytoma, anaplastic astrocytoma, glioblastoma, and glioblastoma multiform; oligodendroglial tumors; and gliomas containing different types of glial cells, such as oligoastrocytoma, anaplastic oligodendroglioma, and oligodendroglioma. Further, the compounds and formulations described herein are utilized to treat both benign and malignant gliomas. In an embodiment, the present invention can be used to treat gliomas that originate from the brain. In another embodiment, the present invention can be used to treat gliomas that originate from the spinal cord. In some embodiments, the compounds disclosed herein are used to treat Grade I, II, III, or IV glioma including, but not limited to, Grade IV glioblastoma and glioblastoma multiform.

In another embodiment, the compounds and formulations described herein are utilized to treat one or more Primary Central Nervous System (CNS) Lymphomas. Primary CNS lymphoma is a rare type of non-Hodgkin Lymphoma (NHL) that is limited to the CNS, which is made up of the brain, spinal cord, eyes, and meninges (the lining of the brain and spinal cord). Most commonly, patients with primary CNS lymphoma have masses found only in the brain. The cell of origin for Primary CNS Lymphoma is a white blood cell called the lymphocyte. Although most times, lymphoma is found in the blood and lymph nodes outside the brain, in Primary CNS Lymphoma, the disease starts in the brain or other nervous system structures and is not found anywhere else in the body.

In another embodiment, the compounds and formulations described herein are utilized to treat Secondary CNS lymphoma. In some embodiments, Secondary CNS lymphomas refer to the situation when the lymphoma starts in another part of your body and then travels to one of the CNS structures, like the spinal cord and brain. In another embodiment, Secondary CNS lymphomas result from cancer of the lung cancer, breast cancer, malignant melanoma, kidney cancer. In a further embodiment, Secondary CNS lymphomas are the most common cause of tumors in the intracranial cavity.

In yet another embodiment is a method for treating a brain tumor or intracranial neoplasm which occurs when abnormal cells form within the brain using the compounds and formulations described herein. In yet another embodiment, the brain tumor is a glioma, meningioma, pituitary adenoma, and nerve sheath tumor.

In yet another embodiment is a method for treating meningeal leukemia and CNS lymphoma and in general neoplasms in the brain using the compounds and formulations described herein.

Irreversible Inhibitor Compounds

In the following description of irreversible kinase inhibitor compounds suitable for use in the methods described herein, definitions of referred-to standard chemistry terms may be found in reference works (if not otherwise defined herein), including Carey and Sundberg “Advanced Organic Chemistry 4th Ed.” Vols. A (2000) and B (2001), Plenum Press, New York. In addition, nucleic acid and amino acid sequences for Btk (e.g., human Btk) are disclosed in, e.g., U.S. Pat. No. 6,326,469. Unless specific definitions are provided, the nomenclature employed in connection with, and the laboratory procedures and techniques of, analytical chemistry, synthetic organic chemistry, and medicinal and pharmaceutical chemistry described herein are those known in the art. Standard techniques can be used for chemical syntheses, chemical analyses, pharmaceutical preparation, formulation, and delivery, and treatment of patients

The inhibitor compounds described herein are selective for kinases having an accessible cysteine residue (such kinases are also known as Accessible Cysteine Kinases, or ACKs) that is able to form a covalent bond with a Michael acceptor moiety on the inhibitor compound. In some embodiments, the cysteine residue is accessible or becomes accessible when the binding site moiety of the irreversible inhibitor binds to the kinase. That is, the binding site moiety of the irreversible inhibitor binds to an active site of the ACK and the Michael acceptor moiety of irreversible inhibitor gains access (in one embodiment the step of binding leads to a conformational change in the ACK, thus exposing the cysteine) or is otherwise exposed to the cysteine residue of the ACK; as a result a covalent bond is formed between the “S” of the cysteine residue and the Michael acceptor of the irreversible inhibitor. Consequently, the binding site moiety of the irreversible inhibitor remains bound or otherwise blocks the active site of the ACK.

In one embodiment, the ACK is Btk, a homolog of Btk or a tyrosine kinase having a cysteine residue in an amino acid sequence position that is homologous to the amino acid sequence position of cysteine 481 in Btk. Inhibitor compounds described herein include a Michael acceptor moiety, a binding site moiety and a linker that links the binding site moiety and the Michael acceptor moiety (and in some embodiments, the structure of the linker provides a conformation, or otherwise directs the Michael acceptor moiety, so as to improve the selectivity of the irreversible inhibitor for a particular ACK).

Generally, an irreversible inhibitor compound used in the methods described herein is identified or characterized in an in vitro assay, e.g., in a cellular biochemical assay or a cellular functional assay. Such assays are useful to determine an in vitro IC₅₀ for an irreversible inhibitor compound.

For example, a cellular kinase assay is used to determine kinase activity after incubation of the kinase in the absence or presence of a range of concentrations of a candidate irreversible inhibitor compound. If the candidate compound is in fact an irreversible inhibitor, kinase activity will not be recovered by repeat washing with inhibitor-free medium. See, e.g., J. B. Smaill, et al. (1999), J. Med. Chem. 42(10):1803-1815. Further, covalent complex formation between a Kinase and a candidate irreversible inhibitor is a useful indicator of irreversible inhibition of the Kinase that is readily determined by a number of methods (e.g., mass spectrometry). For example, some irreversible Kinase-inhibitor compounds form a covalent bond with the aforenoted cysteine residue (e.g., via a Michael reaction).

High throughput assays for many a cellular biochemical assays (e.g., kinase assays) and cellular functional assays (e.g., calcium flux) are documented methodologies. In addition, high throughput screening systems are commercially available (see, e.g., Zymark Corp., Hopkinton, Mass.; Air Technical Industries, Mentor, OH; Beckman Instruments, Inc. Fullerton, Calif.; Precision Systems, Inc., Natick, Mass., etc.). These systems typically automate entire procedures including all sample and reagent pipetting, liquid dispensing, timed incubations, and final readings of the microplate in detector(s) appropriate for the assay. Automated systems thereby allow the identification and characterization of a large number of irreversible compounds.

In some embodiments, irreversible inhibitor compounds are used for the manufacture of a medicament for treating any of the foregoing conditions (e.g. lymphomas, carcinomas, and/or sarcomas).

In some embodiments, the irreversible inhibitor compound used for the methods described herein inhibits a Kinase activity with an in vitro IC₅₀ of less than 10 μM. (e.g., less than 1 μM, less than 0.5 μM, less than 0.4 μM, less than 0.3 μM, less than 0.1, less than 0.08 μM, less than 0.06 μM, less than 0.05 μM, less than 0.04 μM, less than 0.03 μM, less than less than 0.02 μM, less than 0.01, less than 0.008 μM, less than 0.006 μM, less than 0.005 μM, less than 0.004 μM, less than 0.003 μM, less than less than 0.002 μM, less than 0.001, less than 0.00099 μM, less than 0.00098 μM, less than 0.00097 μM, less than 0.00096 μM, less than 0.00095 μM, less than 0.00094 μM, less than 0.00093 μM, less than 0.00092, or less than 0.00090 μM).

Particular Irreversible Inhibitor Compounds for ACKs

Described herein are compounds of any of Formula (A1-A6), Formula (B1-B6), Formula (C1-C6), Formula (D1-D6), Formula (I), or Formula (VII). Also described herein are pharmaceutically acceptable salts, pharmaceutically acceptable solvates, pharmaceutically active metabolites, and pharmaceutically acceptable prodrugs of such compounds. Pharmaceutical compositions that include at least one such compound or a pharmaceutically acceptable salt, pharmaceutically acceptable solvate, pharmaceutically active metabolite or pharmaceutically acceptable prodrug of such compound, are provided. In some embodiments, when compounds disclosed herein contain an oxidizable nitrogen atom, the nitrogen atom is optionally converted to an N-oxide. In certain embodiments, isomers and chemically protected forms of compounds having a structure represented by any of Formula (A1-A6), Formula (B1-B6), Formula (C1-C6), Formula (D1-D6), Formula (I), or Formula (VII), are also provided.

In one aspect are compounds (including irreversible inhibitors of ACKs, including Btk and its cysteine homologs) having the structure of Formula (I):

wherein

-   -   L_(a) is CH₂, O, NH or S;     -   Ar is a substituted or unsubstituted aryl, or a substituted or         unsubstituted heteroaryl; and either     -   (a) Y is an optionally substituted group selected from among         alkylene, heteroalkylene, arylene, heteroarylene,         alkylenearylene, alkyleneheteroarylene, alkylenecycloalkylene         and alkyleneheterocycloalkylene;     -   Z is C(═O), NHC(═O), NR^(a)C(═O), NR^(a)S(═O)_(x), where x is 1         or 2, and R^(a) is H, substituted or unsubstituted alkyl,         substituted or unsubstituted cycloalkyl; and either     -   (i) R₇ and R₈ are H;     -   R₆ is H, substituted or unsubstituted C₁-C₄alkyl, substituted or         unsubstituted C₁-C₄heteroalkyl, C₁-C₈alkylaminoalkyl, C₁-C₈         hydroxyalkylaminoalkyl, C₁-C₈ alkoxyalkylaminoalkyl, substituted         or unsubstituted C₃-C₆cycloalkyl, substituted or unsubstituted         C₁-C₈alkylC₃-C₆cycloalkyl, substituted or unsubstituted aryl,         substituted or unsubstituted C₂-C₈heterocycloalkyl, substituted         or unsubstituted heteroaryl, C₁-C₄alkyl(aryl),         C₁-C₄alkyl(heteroaryl), C₁-C₈alkylethers, C₁-C₈alkylamides, or         C₁-C₄alkyl(C₂-C₈heterocycloalkyl);     -   (ii) R₆ and R₈ are H;     -   R₇ is H, substituted or unsubstituted C₁-C₄alkyl, substituted or         unsubstituted C₁-C₄heteroalkyl, C₁-C₈alkylaminoalkyl, C₁-C₈         hydroxyalkylaminoalkyl, C₁-C₈ alkoxyalkylaminoalkyl, substituted         or unsubstituted C₃-C₆cycloalkyl, substituted or unsubstituted         C₁-C₈alkylC₃-C₆cycloalkyl, substituted or unsubstituted aryl,         substituted or unsubstituted C₂-C₈heterocycloalkyl, substituted         or unsubstituted heteroaryl, C₁-C₄alkyl(aryl),         C₁-C₄alkyl(heteroaryl), C₁-C₈alkylethers, C₁-C₈alkylamides, or         C₁-C₄alkyl(C₂-C₈heterocycloalkyl); or     -   (iii) R₇ and R₈ taken together form a bond;     -   R₆ is H, substituted or unsubstituted C₁-C₄alkyl, substituted or         unsubstituted C₁-C₄heteroalkyl, C₁-C₈alkylaminoalkyl, C₁-C₈         hydroxyalkylaminoalkyl, C₁-C₈ alkoxyalkylaminoalkyl, substituted         or unsubstituted C₃-C₆cycloalkyl, substituted or unsubstituted         C₁-C₈alkylC₃-C₆cycloalkyl, substituted or unsubstituted aryl,         substituted or unsubstituted C₂-C₈heterocycloalkyl, substituted         or unsubstituted heteroaryl, C₁-C₄alkyl(aryl),         C₁-C₄alkyl(heteroaryl), C₁-C₈alkylethers, C₁-C₈alkylamides, or         C₁-C₄alkyl(C₂-C₈heterocycloalkyl); or     -   (b) Y is an optionally substituted group selected from         cycloalkylene or heterocycloalkylene;     -   Z is C(═O), NHC(═O), NR^(a)C(═O), NR^(a)S(═O)_(x), where x is 1         or 2, and R^(a) is H, substituted or unsubstituted alkyl,         substituted or unsubstituted cycloalkyl; and either     -   (i) R₇ and R₈ are H;     -   R₆ is substituted or unsubstituted C₁-C₄heteroalkyl, C₁-C₈         hydroxyalkylaminoalkyl, C₁-C₈ alkoxyalkylaminoalkyl, substituted         or unsubstituted C₃-C₆cycloalkyl, substituted or unsubstituted         C₁-C₈alkylC₃-C₆cycloalkyl, substituted or unsubstituted aryl,         substituted or unsubstituted C₂-C₈heterocycloalkyl, substituted         or unsubstituted heteroaryl, C₁-C₄alkyl(aryl),         C₁-C₄alkyl(heteroaryl), C₁-C₈alkylethers, C₁-C₈alkylamides, or         C₁-C₄alkyl(C₂-C₈heterocycloalkyl);     -   (ii) R₆ and R₈ are H;     -   R₇ is substituted or unsubstituted C₁-C₄heteroalkyl, C₁-C₈         hydroxyalkylaminoalkyl, C₁-C₈ alkoxyalkylaminoalkyl, substituted         or unsubstituted C₃-C₆cycloalkyl, substituted or unsubstituted         C₁-C₈alkylC₃-C₆cycloalkyl, substituted or unsubstituted aryl,         substituted or unsubstituted C₂-C₈heterocycloalkyl, substituted         or unsubstituted heteroaryl, C₁-C₄alkyl(aryl),         C₁-C₄alkyl(heteroaryl), C₁-C₈alkylethers, C₁-C₈alkylamides, or         C₁-C₄alkyl(C₂-C₈heterocycloalkyl); or     -   (iii) R₇ and R₈ taken together form a bond;     -   R₆ is substituted or unsubstituted C₁-C₄alkyl, substituted or         unsubstituted C₁-C₄heteroalkyl, C₁-C₈alkylaminoalkyl,         C₁-C₈hydroxyalkylaminoalkyl, C₁-C₈alkoxyalkylaminoalkyl,         substituted or unsubstituted C₃-C₆cycloalkyl, substituted or         unsubstituted C₁-C₈alkylC₃-C₆cycloalkyl, substituted or         unsubstituted aryl, substituted or unsubstituted         C₂-C₈heterocycloalkyl, substituted or unsubstituted heteroaryl,         C₁-C₄alkyl(aryl), C₁-C₄alkyl(heteroaryl), C₁-C₈alkylethers,         C₁-C₈alkylamides, or C₁-C₄alkyl(C₂-C₈heterocycloalkyl); and         pharmaceutically active metabolites, or pharmaceutically         acceptable solvates, pharmaceutically acceptable salts, or         pharmaceutically acceptable prodrugs thereof.

In another embodiment are provided pharmaceutically acceptable salts of compounds of Formula (I). By way of example only, are salts of an amino group formed with inorganic acids such as hydrochloric acid, hydrobromic acid, phosphoric acid, sulfuric acid and perchloric acid or with organic acids such as acetic acid, oxalic acid, maleic acid, tartaric acid, citric acid, succinic acid or malonic acid. Further salts include those in which the counterion is an anion, such as adipate, alginate, ascorbate, aspartate, benzenesulfonate, benzoate, bisulfate, borate, butyrate, camphorate, camphorsulfonate, citrate, cyclopentanepropionate, digluconate, dodecylsulfate, ethanesulfonate, formate, fumarate, glucoheptonate, glycerophosphate, gluconate, hemisulfate, heptanoate, hexanoate, hydroiodide, 2-hydroxy-ethanesulfonate, lactobionate, lactate, laurate, lauryl sulfate, malate, maleate, malonate, methanesulfonate, 2-naphthalenesulfonate, nicotinate, nitrate, oleate, oxalate, palmitate, pamoate, pectinate, persulfate, 3-phenylpropionate, phosphate, picrate, pivalate, propionate, stearate, succinate, sulfate, tartrate, thiocyanate, p-toluenesulfonate, undecanoate, and valerate. Further salts include those in which the counterion is an cation, such as sodium, lithium, potassium, calcium, magnesium, ammonium, and quaternary ammonium (substituted with at least one organic moiety) cations.

In another embodiment are pharmaceutically acceptable esters of compounds of Formula (I), including those in which the ester group is selected from a formate, acetate, propionate, butyrate, acrylate and ethylsuccinate.

In another embodiment are pharmaceutically acceptable carbamates of compounds of Formula (I). In another embodiment are pharmaceutically acceptable N-acyl derivatives of compounds of Formula (I). Examples of N-acyl groups include N-acetyl and N-ethoxycarbonyl groups.

For any and all of the embodiments, substituents can be selected from among from a subset of the listed alternatives. For example, in some embodiments, L_(a) is CH₂, O, or NH. In other embodiments, L_(a) is O or NH. In yet other embodiments, L_(a) is O.

In some embodiments, Ar is a substituted or unsubstituted aryl. In yet other embodiments, Ar is a 6-membered aryl. In some other embodiments, Ar is phenyl.

In some embodiments, x is 2. In yet other embodiments, Z is C(═O), OC(═O), NHC(═O), S(═O)_(x), OS(═O)_(x), or NHS(═O)_(x). In some other embodiments, Z is C(═O), NHC(═O), or NCH₃C(═O).

In some embodiments Y is an optionally substituted group selected from among alkylene, heteroalkylene, arylene, heteroarylene, alkylenearylene, alkyleneheteroarylene, and alkyleneheterocycloalkylene.

In some embodiments, Z is C(═O), NHC(═O), NR^(a)C(═O), NR^(a)S(═O)_(x), where x is 1 or 2, and R^(a) is H, substituted or unsubstituted alkyl, substituted or unsubstituted cycloalkyl.

In some embodiments, R₇ and R₈ are H; and R₆ is H, substituted or unsubstituted C₁-C₄alkyl, substituted or unsubstituted C₁-C₄heteroalkyl, C₁-C₈alkylaminoalkyl, C₁-C₈hydroxyalkylaminoalkyl, C₁-C₈alkoxyalkylaminoalkyl, substituted or unsubstituted C₃-C₆cycloalkyl, substituted or unsubstituted C₁-C₈alkylC₃-C₆cycloalkyl, substituted or unsubstituted aryl, substituted or unsubstituted C₂-C₈heterocycloalkyl, substituted or unsubstituted heteroaryl, C₁-C₄alkyl(aryl), C₁-C₄alkyl(heteroaryl), C₁-C₈alkylethers, C₁-C₈alkylamides, or C₁-C₄alkyl(C₂-C₈heterocycloalkyl). In other embodiments, R₆ and R₈ are H; and R₇ is H, substituted or unsubstituted C₁-C₄alkyl, substituted or unsubstituted C₁-C₄heteroalkyl, C₁-C₈alkylaminoalkyl, C₁-C₈hydroxyalkylaminoalkyl, C₁-C₈alkoxyalkylaminoalkyl, substituted or unsubstituted C₃-C₆cycloalkyl, substituted or unsubstituted C₁-C₈alkylC₃-C₆cycloalkyl, substituted or unsubstituted aryl, substituted or unsubstituted C₂-C₈heterocycloalkyl, substituted or unsubstituted heteroaryl, C₁-C₄alkyl(aryl), C₁-C₄alkyl(heteroaryl), C₁-C₈alkylethers, C₁-C₈alkylamides, or C₁-C₄alkyl(C₂-C₈heterocycloalkyl). In yet further embodiments, R₇ and R₈ taken together form a bond; and R₆ is H, substituted or unsubstituted C₁-C₄alkyl, substituted or unsubstituted C₁-C₄heteroalkyl, C₁-C₈alkylaminoalkyl, C₁-C₈hydroxyalkylaminoalkyl, C₁-C₈alkoxyalkylaminoalkyl, substituted or unsubstituted C₃-C₆cycloalkyl, substituted or unsubstituted C₁-C₈alkylC₃-C₆cycloalkyl, substituted or unsubstituted aryl, substituted or unsubstituted C₂-C₈heterocycloalkyl, substituted or unsubstituted heteroaryl, C₁-C₄alkyl(aryl), C₁-C₄alkyl(heteroaryl), C₁-C₈alkylethers, C₁-C₈alkylamides, or C₁-C₄alkyl(C₂-C₈heterocycloalkyl).

In some embodiments, Y is an optionally substituted group selected from cycloalkylene or heterocycloalkylene.

In some embodiments, Z is C(═O), NHC(═O), NR^(a)C(═O), NR^(a)S(═O)_(x), where x is 1 or 2, and R^(a) is H, substituted or unsubstituted alkyl, substituted or unsubstituted cycloalkyl.

In some embodiments, R₇ and R₈ are H; and R₆ is substituted or unsubstituted C₁-C₄heteroalkyl, C₁-C₈hydroxyalkylaminoalkyl, C₁-C₈alkoxyalkylaminoalkyl, substituted or unsubstituted C₃-C₆cycloalkyl, substituted or unsubstituted C₁-C₈alkylC₃-C₆cycloalkyl, substituted or unsubstituted aryl, substituted or unsubstituted C₂-C₈heterocycloalkyl, substituted or unsubstituted heteroaryl, C₁-C₄alkyl(aryl), C₁-C₄alkyl(heteroaryl), C₁-C₈alkylethers, C₁-C₈alkylamides, or C₁-C₄alkyl(C₂-C₈heterocycloalkyl). In other embodiments, R₆ and R₈ are H; and R₇ is substituted or unsubstituted C₁-C₄heteroalkyl, C₁-C₈hydroxyalkylaminoalkyl, C₁-C₈alkoxyalkylaminoalkyl, substituted or unsubstituted C₃-C₆cycloalkyl, substituted or unsubstituted C₁-C₈alkylC₃-C₆cycloalkyl, substituted or unsubstituted aryl, substituted or unsubstituted C₂-C₈heterocycloalkyl, substituted or unsubstituted heteroaryl, C₁-C₄alkyl(aryl), C₁-C₄alkyl(heteroaryl), C₁-C₈alkylethers, C₁-C₈alkylamides, or C₁-C₄alkyl(C₂-C₈heterocycloalkyl). In further embodiments, R₇ and R₈ taken together form a bond; and R₆ is substituted or unsubstituted C₁-C₄alkyl, substituted or unsubstituted C₁-C₄heteroalkyl, C₁-C₈alkylaminoalkyl, C₁-C₈hydroxyalkylaminoalkyl, C₁-C₈alkoxyalkylaminoalkyl, substituted or unsubstituted C₃-C₆cycloalkyl, substituted or unsubstituted C₁-C₈alkylC₃-C₆cycloalkyl, substituted or unsubstituted aryl, substituted or unsubstituted C₂-C₈heterocycloalkyl, substituted or unsubstituted heteroaryl, C₁-C₄alkyl(aryl), C₁-C₄alkyl(heteroaryl), C₁-C₈alkylethers, C₁-C₈alkylamides, or C₁-C₄alkyl(C₂-C₈heterocycloalkyl).

In one aspect are compounds (including irreversible inhibitors of ACKs, including Btk and its cysteine homologs) having the structure of Formula (VII):

-   -   wherein

-   -    is a moiety that binds to the active site of a kinase,         including a tyrosine kinase, further including a Btk kinase         cysteine homolog;     -   Y is an optionally substituted group selected from among         alkylene, heteroalkylene, arylene, heteroarylene,         heterocycloalkylene, cycloalkylene, alkylenearylene,         alkyleneheteroarylene, alkylenecycloalkylene, and         alkyleneheterocycloalkylene;     -   Z is C(═O), OC(═O), NHC(═O), NCH₃C(═O), C(═S), S(═O)_(x),         OS(═O)_(x), NHS(═O)_(x), where x is 1 or 2;     -   R₇ and R₈ are independently selected from among H, unsubstituted         C₁-C₄ alkyl, substituted

C₁-C₄alkyl, unsubstituted C₁-C₄heteroalkyl, substituted C₁-C₄heteroalkyl, unsubstituted C₃-C₆cycloalkyl, substituted C₃-C₆cycloalkyl, unsubstituted C₂-C₆heterocycloalkyl, and substituted C₂-C₆heterocycloalkyl; or

-   -   R₇ and R₈ taken together form a bond; and     -   R₆ is H, substituted or unsubstituted C₁-C₄alkyl, substituted or         unsubstituted C₁-C₄heteroalkyl, C₁-C₆alkoxyalkyl,         C₁-C₈alkylaminoalkyl, C₁-C₈hydroxyalkylaminoalkyl,         C₁-C₈alkoxyalkylaminoalkyl, substituted or unsubstituted         C₃-C₆cycloalkyl, substituted or unsubstituted aryl, substituted         or unsubstituted C₂-C₈heterocycloalkyl, substituted or         unsubstituted heteroaryl, C₁-C₄alkyl(aryl),         C₁-C₄alkyl(heteroaryl), C₁-C₄alkyl(C₃-C₈cycloalkyl), or         C₁-C₄alkyl(C₂-C₈heterocycloalkyl); and         pharmaceutically active metabolites, or pharmaceutically         acceptable solvates, pharmaceutically acceptable salts, or         pharmaceutically acceptable prodrugs thereof.

In another embodiment are provided pharmaceutically acceptable salts of compounds of Formula (VII). By way of example only, are salts of an amino group formed with inorganic acids such as hydrochloric acid, hydrobromic acid, phosphoric acid, sulfuric acid and perchloric acid or with organic acids such as acetic acid, oxalic acid, maleic acid, tartaric acid, citric acid, succinic acid or malonic acid. Further salts include those in which the counterion is an anion, such as adipate, alginate, ascorbate, aspartate, benzenesulfonate, benzoate, bisulfate, borate, butyrate, camphorate, camphorsulfonate, citrate, cyclopentanepropionate, digluconate, dodecylsulfate, ethanesulfonate, formate, fumarate, glucoheptonate, glycerophosphate, gluconate, hemisulfate, heptanoate, hexanoate, hydroiodide, 2-hydroxy-ethanesulfonate, lactobionate, lactate, laurate, lauryl sulfate, malate, maleate, malonate, methanesulfonate, 2-naphthalenesulfonate, nicotinate, nitrate, oleate, oxalate, palmitate, pamoate, pectinate, persulfate, 3-phenylpropionate, phosphate, picrate, pivalate, propionate, stearate, succinate, sulfate, tartrate, thiocyanate, p-toluenesulfonate, undecanoate, and valerate. Further salts include those in which the counterion is an cation, such as sodium, lithium, potassium, calcium, magnesium, ammonium, and quaternary ammonium (substituted with at least one organic moiety) cations.

In another embodiment are pharmaceutically acceptable esters of compounds of Formula (VII), including those in which the ester group is selected from a formate, acetate, propionate, butyrate, acrylate and ethylsuccinate.

In another embodiment are pharmaceutically acceptable carbamates of compounds of Formula (VII). In another embodiment are pharmaceutically acceptable N-acyl derivatives of compounds of Formula (VII). Examples of N-acyl groups include N-acetyl and N-ethoxycarbonyl groups.

In some embodiments, x is 2. In yet other embodiments, Z is C(═O), OC(═O), NHC(═O), S(═O)_(x), OS(═O)_(x), or NHS(═O)_(x). In some other embodiments, Z is C(═O), NHC(═O), or S(═O)₂.

In some embodiments, R₇ and R₈ are independently selected from among H, unsubstituted C₁-C₄ alkyl, substituted C₁-C₄alkyl, unsubstituted C₁-C₄heteroalkyl, and substituted C₁-C₄heteroalkyl; or R₇ and R₈ taken together form a bond. In yet other embodiments, each of R₇ and R₈ is H; or R₇ and R₈ taken together form a bond.

In some embodiments, R₆ is H, substituted or unsubstituted C₁-C₄alkyl, substituted or unsubstituted C₁-C₄heteroalkyl, C₁-C₆alkoxyalkyl, C₁-C₈alkylaminoalkyl, substituted or unsubstituted aryl, substituted or unsubstituted heteroaryl, C₁-C₄alkyl(aryl), C₁-C₄alkyl(heteroaryl), C₁-C₄alkyl(C₃-C₈cycloalkyl), or C₁-C₄alkyl(C₂-C₈heterocycloalkyl). In some other embodiments, R₆ is H, substituted or unsubstituted C₁-C₄alkyl, substituted or unsubstituted C₁-C₄heteroalkyl, C₁-C₆alkoxyalkyl, C₁-C₂alkyl-N(C₁-C₃alkyl)₂, C₁-C₄alkyl(aryl), C₁-C₄alkyl(heteroaryl), C₁-C₄alkyl(C₃-C₈cycloalkyl), or C₁-C₄alkyl(C₂-C₈heterocycloalkyl). In yet other embodiments, R₆ is H, substituted or unsubstituted C₁-C₄alkyl, —CH₂—O—(C₁-C₃alkyl), —CH₂—N(C₁-C₃alkyl)₂, C₁-C₄alkyl(phenyl), or C₁-C₄alkyl(5- or 6-membered heteroaryl). In yet other embodiments, R₆ is H, substituted or unsubstituted C₁-C₄alkyl, —CH₂—O—(C₁-C₃alkyl), —CH₂—(C₁-C₆alkylamino), C₁-C₄alkyl(phenyl), or C₁-C₄alkyl(5- or 6-membered heteroaryl). In some embodiments, R₆ is H, substituted or unsubstituted C₁-C₄alkyl, —CH₂—O—(C₁-C₃alkyl), —CH₂—N(C₁-C₃alkyl)₂, C₁-C₄alkyl(phenyl), or C₁-C₄alkyl(5- or 6-membered heteroaryl containing 1 or 2 N atoms), or C₁-C₄alkyl(5- or 6-membered heterocycloalkyl containing 1 or 2 N atoms).

In some embodiments, Y is an optionally substituted group selected from among alkylene, heteroalkylene, arylene, heteroarylene, heterocycloalkylene, cycloalkylene, alkylenearylene, alkyleneheteroarylene, alkylenecycloalkylene, and alkyleneheterocycloalkylene. In other embodiments, Y is an optionally substituted group selected from among C₁-C₆alkylene, C₁-C₆heteroalkylene, 4-, 5-, 6-, or 7-membered cycloalkylene, and 4-, 5-, 6-, or 7-membered heterocycloalkylene. In yet other embodiments, Y is an optionally substituted group selected from among C₁-C₆alkylene, C₁-C₆heteroalkylene, 5- or 6-membered cycloalkylene, and 5- or 6-membered heterocycloalkylene containing 1 or 2 N atoms. In some other embodiments, Y is a 5- or 6-membered cycloalkylene, or a 5- or 6-membered heterocycloalkylene containing 1 or 2 N atoms. In some embodiments, Y is a 4-, 5-, 6-, or 7-membered cycloalkylene ring; or Y is a 4-, 5-, 6-, or 7-membered heterocycloalkylene ring.

In one aspect are compounds (including irreversible inhibitors of ACKs, including Btk and its cysteine homologs) having the structure of Formula (A1):

wherein

-   -   A is independently selected from N or CR₅;     -   R₁ is H, L₂-(substituted or unsubstituted alkyl),         L₂-(substituted or unsubstituted cycloalkyl), L₂-(substituted or         unsubstituted alkenyl), L₂-(substituted or unsubstituted         cycloalkenyl), L₂-(substituted or unsubstituted heterocycle),         L₂-(substituted or unsubstituted heteroaryl), or L₂-(substituted         or unsubstituted aryl), where L₂ is a bond, O, S, —S(═O),         —S(═O)₂, C(═O), -(substituted or unsubstituted C₁-C₆ alkylene),         or -(substituted or unsubstituted C₂-C₆ alkenylene);     -   R₂ and R₃ are independently selected from H, lower alkyl and         substituted lower alkyl;     -   R₄ is L₃-X-L₄-G, wherein,         -   L₃ is optional, and when present is a bond, or an optionally             substituted group selected from alkylene, heteroalkylene,             arylene, heteroarylene, alkylarylene, alkylheteroarylene, or             alkylheterocycloalkylene;         -   X is optional, and when present is a bond, O, —C(═O), S,             —S(═O), —S(═O)₂, —NH, —NR₉, —NHC(O), —C(O)NH, —NR₉C(O),             —C(O)NR₉, —S(═O)₂NH, —NHS(═O)₂, —S(═O)₂NR₉—, —NR₉S(═O)₂,             —OC(O)NH—, —NHC(O)O—, —OC(O)NR₉—, —NR₉C(O)O—, —CH═NO—,             —ON═CH—, —NR₁₀C(O)NR₁₀—, heteroarylene, arylene,             —NR₁₀C(═NR₁₁)NR₁₀—, —NR₁₀C(═NR₁₁)—, —C(═NR₁₁)NR₁₀—,             —OC(═NR₁₁)—, or —C(═NR₁₁)O—;         -   L₄ is optional, and when present is a bond, substituted or             unsubstituted alkylene, substituted or unsubstituted             cycloalkylene, substituted or unsubstituted alkenylene,             substituted or unsubstituted alkynylene, substituted or             unsubstituted arylene, substituted or unsubstituted             heteroarylene, substituted or unsubstituted heterocyclene;         -   or L₃, X and L₄ taken together form a nitrogen containing             heterocyclic ring, or an optionally substituted group             selected from alkyl, heteroalkyl, aryl, heteroaryl,             alkylaryl, alkylheteroaryl, or alkylheterocycloalkyl;             -   G is

-   -    where R^(b) is H, substituted or unsubstituted alkyl,         substituted or unsubstituted cycloalkyl; and either         -   R₇ and R₈ are H;             -   R₆ is H, substituted or unsubstituted C₁-C₄alkyl,                 substituted or unsubstituted C₁-C₄heteroalkyl,                 C₁-C₈alkylaminoalkyl, C₁-C₈hydroxyalkylaminoalkyl,                 C₁-C₈alkoxyalkylaminoalkyl, substituted or unsubstituted                 C₃-C₆cycloalkyl, substituted or unsubstituted                 C₁-C₈alkylC₃-C₆cycloalkyl, substituted or unsubstituted                 aryl, substituted or unsubstituted                 C₂-C₈heterocycloalkyl, substituted or unsubstituted                 heteroaryl, C₁-C₄alkyl(aryl), C₁-C₄alkyl(heteroaryl),                 C₁-C₈alkylethers, C₁-C₈alkylamides, or                 C₁-C₄alkyl(C₂-C₈heterocycloalkyl);             -   R₆ and R₈ are H;                 -   R₇ is H, substituted or unsubstituted C₁-C₄alkyl,                     substituted or unsubstituted C₁-C₄heteroalkyl,                     C₁-C₈alkylaminoalkyl, C₁-C₈hydroxyalkylaminoalkyl,                     C₁-C₈alkoxyalkylaminoalkyl, substituted or                     unsubstituted C₃-C₆cycloalkyl, substituted or                     unsubstituted C₁-C₈alkylC₃-C₆cycloalkyl, substituted                     or unsubstituted aryl, substituted or unsubstituted                     C₂-C₈heterocycloalkyl, substituted or unsubstituted                     heteroaryl, C₁-C₄alkyl(aryl),                     C₁-C₄alkyl(heteroaryl), C₁-C₈alkylethers,                     C₁-C₈alkylamides, or                     C₁-C₄alkyl(C₂-C₈heterocycloalkyl); or             -   R₇ and R₈ taken together form a bond;                 -   R₆ is H, substituted or unsubstituted C₁-C₄alkyl,                     substituted or unsubstituted C₁-C₄heteroalkyl,                     C₁-C₈alkylaminoalkyl, C₁-C₈hydroxyalkylaminoalkyl,                     C₁-C₈alkoxyalkylaminoalkyl, substituted or                     unsubstituted C₃-C₆cycloalkyl, substituted or                     unsubstituted C₁-C₈alkylC₃-C₆cycloalkyl, substituted                     or unsubstituted aryl, substituted or unsubstituted                     C₂-C₈heterocycloalkyl, substituted or unsubstituted                     heteroaryl, C₁-C₄alkyl(aryl),                     C₁-C₄alkyl(heteroaryl), C₁-C₈alkylethers,                     C₁-C₈alkylamides, or                     C₁-C₄alkyl(C₂-C₈heterocycloalkyl); or     -   R₅ is H, halogen, -L₆-(substituted or unsubstituted C₁-C₃         alkyl), -L₆-(substituted or unsubstituted C₂-C₄ alkenyl),         -L₆-(substituted or unsubstituted heteroaryl), or         -L₆-(substituted or unsubstituted aryl), wherein L₆ is a bond,         O, S, —S(═O), S(═O)₂, NH, C(O), —NHC(O)O, —OC(O)NH, —NHC(O), or         —C(O)NH;     -   R₉ is selected from among H, substituted or unsubstituted lower         alkyl, and substituted or unsubstituted lower cycloalkyl;     -   each R₁₀ is independently H, substituted or unsubstituted lower         alkyl, or substituted or unsubstituted lower cycloalkyl; or     -   two R₁₀ groups can together form a 5-, 6-, 7-, or 8-membered         heterocyclic ring; or     -   R₁₀ and R₁₁ can together form a 5-, 6-, 7-, or 8-membered         heterocyclic ring; or     -   R₁₁ is selected from H, —S(═O)₂R₈, —S(═O)₂NH₂, —C(O)R₈, —CN,         —NO₂, heteroaryl, or heteroalkyl; and pharmaceutically active         metabolites, pharmaceutically acceptable solvates,         pharmaceutically acceptable salts, or pharmaceutically         acceptable prodrugs thereof.

In some embodiments, A is independently selected from N. In some embodiments R₁ is L or unsubstituted heteroaryl), or L₂-(substituted or unsubstituted aryl), where L₂ is a bond, O, S, —S(═O), —S(═O)₂, C(═O), -(substituted or unsubstituted C₁-C₆ alkylene), or -(substituted or unsubstituted C₂-C₆ alkenylene). In a further embodiment, R₁ is L₂-(substituted or unsubstituted aryl) and L₂ is a bond. In a further embodiment, R₁ is L₂-(substituted aryl) wherein L₂ is a bond and aryl is substituted with L3-(substituted or unsubstituted heteroaryl) or L₃-(substituted or unsubstituted aryl). In a further embodiment, L₃ is a bond, O, S, NHC(O), C(O)NH.

In some embodiments, L₃, X and L₄ taken together form a nitrogen containing heterocyclic ring. In a further embodiment L₃, X and L₄ taken together form a pyrrolidine ring or a piperidine ring. In yet a further embodiment L₃, X and L₄ taken together form a piperidine ring.

In some embodiments, G is

In some embodiments G is

In some embodiments, R₆, R₇ and R₈ are H.

In another embodiment are provided pharmaceutically acceptable salts of compounds of Formula (A1). By way of example only, are salts of an amino group formed with inorganic acids such as hydrochloric acid, hydrobromic acid, phosphoric acid, sulfuric acid and perchloric acid or with organic acids such as acetic acid, oxalic acid, maleic acid, tartaric acid, citric acid, succinic acid or malonic acid. Further salts include those in which the counterion is an anion, such as adipate, alginate, ascorbate, aspartate, benzenesulfonate, benzoate, bisulfate, borate, butyrate, camphorate, camphorsulfonate, citrate, cyclopentanepropionate, digluconate, dodecylsulfate, ethanesulfonate, formate, fumarate, glucoheptonate, glycerophosphate, gluconate, hemisulfate, heptanoate, hexanoate, hydroiodide, 2-hydroxy-ethanesulfonate, lactobionate, lactate, laurate, lauryl sulfate, malate, maleate, malonate, methanesulfonate, 2-naphthalenesulfonate, nicotinate, nitrate, oleate, oxalate, palmitate, pamoate, pectinate, persulfate, 3-phenylpropionate, phosphate, picrate, pivalate, propionate, stearate, succinate, sulfate, tartrate, thiocyanate, p-toluenesulfonate, undecanoate, and valerate. Further salts include those in which the counterion is an cation, such as sodium, lithium, potassium, calcium, magnesium, ammonium, and quaternary ammonium (substituted with at least one organic moiety) cations.

In another embodiment are pharmaceutically acceptable esters of compounds of Formula (A1), including those in which the ester group is selected from a formate, acetate, propionate, butyrate, acrylate and ethylsuccinate.

In another embodiment are pharmaceutically acceptable carbamates of compounds of Formula (A1). In another embodiment are pharmaceutically acceptable N-acyl derivatives of compounds of Formula (A1). Examples of N-acyl groups include N-acetyl and N-ethoxycarbonyl groups.

In a further or alternative embodiment, the compound of Formula (A1) has the following structure of Formula (B1):

wherein:

-   -   Y is an optionally substituted group selected from among         alkylene, heteroalkylene, arylene, heteroarylene,         alkylenearylene, alkyleneheteroarylene, and         alkyleneheterocycloalkylene;     -   each R_(a) is independently H, halogen, —CF₃, —CN, —NO₂, OH,         NH₂, -L_(a)-(substituted or unsubstituted alkyl),         -L_(a)-(substituted or unsubstituted alkenyl),         -L_(a)-(substituted or unsubstituted heteroaryl), or         -L_(a)-(substituted or unsubstituted aryl), wherein L_(a) is a         bond, O, S, —S(═O), —S(═O)₂, NH, C(O), CH₂, —NHC(O)O, —NHC(O),         or —C(O)NH;     -   G is

-   -    where R^(b) is H, substituted or unsubstituted alkyl,         substituted or unsubstituted cycloalkyl; and either     -   R₇ and R₈ are H;         -   R₆ is H, substituted or unsubstituted C₁-C₄alkyl,             substituted or unsubstituted C₁-C₄heteroalkyl,             C₁-C₈alkylaminoalkyl, C₁-C₈hydroxyalkylaminoalkyl,             C₁-C₈alkoxyalkylaminoalkyl, substituted or unsubstituted             C₃-C₆cycloalkyl, substituted or unsubstituted             C₁-C₈alkylC₃-C₆cycloalkyl, substituted or unsubstituted             aryl, substituted or unsubstituted C₂-C₈heterocycloalkyl,             substituted or unsubstituted heteroaryl, C₁-C₄alkyl(aryl),             C₁-C₄alkyl(heteroaryl), C₁-C₈alkylethers, C₁-C₈alkylamides,             or C₁-C₄alkyl(C₂-C₈heterocycloalkyl);     -   R₆ and R₈ are H;         -   R₇ is H, substituted or unsubstituted C₁-C₄alkyl,             substituted or unsubstituted C₁-C₄heteroalkyl,             C₁-C₈alkylaminoalkyl, C₁-C₈hydroxyalkylaminoalkyl,             C₁-C₈alkoxyalkylaminoalkyl, substituted or unsubstituted             C₃-C₆cycloalkyl, substituted or unsubstituted             C₁-C₈alkylC₃-C₆cycloalkyl, substituted or unsubstituted             aryl, substituted or unsubstituted C₂-C₈heterocycloalkyl,             substituted or unsubstituted heteroaryl, C₁-C₄alkyl(aryl),             C₁-C₄alkyl(heteroaryl), C₁-C₈alkylethers, C₁-C₈alkylamides,             or C₁-C₄alkyl(C₂-C₈heterocycloalkyl); or     -   R₇ and R₈ taken together form a bond;         -   R₆ is H, substituted or unsubstituted C₁-C₄alkyl,             substituted or unsubstituted C₁-C₄heteroalkyl,             C₁-C₈alkylaminoalkyl, C₁-C₈hydroxyalkylaminoalkyl,             C₁-C₈alkoxyalkylaminoalkyl, substituted or unsubstituted             C₃-C₆cycloalkyl, substituted or unsubstituted             C₁-C₈alkylC₃-C₆cycloalkyl, substituted or unsubstituted             aryl, substituted or unsubstituted C₂-C₈heterocycloalkyl,             substituted or unsubstituted heteroaryl, C₁-C₄alkyl(aryl),             C₁-C₄alkyl(heteroaryl), C₁-C₈alkylethers, C₁-C₈alkylamides,             or C₁-C₄alkyl(C₂-C₈heterocycloalkyl);     -   R₁₂ is H or lower alkyl; or     -   Y and R₁₂ taken together form a 4-, 5-, or 6-membered         heterocyclic ring; and     -   pharmaceutically acceptable active metabolites, pharmaceutically         acceptable solvates, pharmaceutically acceptable salts, or         pharmaceutically acceptable prodrugs thereof.

In further or alternative embodiments, G is selected from among

where R is H, alkyl, alkylhydroxy, heterocycloalkyl, heteroaryl, alkylalkoxy, alkylalkoxyalkyl.

In further or alternative embodiments,

is selected from among

In further or alternative embodiment, the compound of Formula (B1) has the following structure of Formula (C1):

-   -   Y is an optionally substituted group selected from among         alkylene, heteroalkylene, arylene, heteroarylene, alkylarylene,         alkylheteroarylene, and alkylheterocycloalkylene;     -   R₁₂ is H or lower alkyl; or     -   Y and R₁₂ taken together form a 4-, 5-, or 6-membered         heterocyclic ring;     -   G is

-   -    where R^(b) is H, substituted or unsubstituted alkyl,         substituted or unsubstituted cycloalkyl; and either     -   R₇ and R₈ are H;         -   R₆ is H, substituted or unsubstituted C₁-C₄alkyl,             substituted or unsubstituted C₁-C₄heteroalkyl,             C₁-C₈alkylaminoalkyl, C₁-C₈hydroxyalkylaminoalkyl,             C₁-C₈alkoxyalkylaminoalkyl, substituted or unsubstituted             C₃-C₆cycloalkyl, substituted or unsubstituted             C₁-C₈alkylC₃-C₆cycloalkyl, substituted or unsubstituted             aryl, substituted or unsubstituted C₂-C₈heterocycloalkyl,             substituted or unsubstituted heteroaryl, C₁-C₄alkyl(aryl),             C₁-C₄alkyl(heteroaryl), C₁-C₈alkylethers, C₁-C₈alkylamides,             or C₁-C₄alkyl(C₂-C₈heterocycloalkyl);     -   R₆ and R₈ are H;         -   R₇ is H, substituted or unsubstituted C₁-C₄alkyl,             substituted or unsubstituted C₁-C₄heteroalkyl,             C₁-C₈alkylaminoalkyl, C₁-C₈hydroxyalkylaminoalkyl,             C₁-C₈alkoxyalkylaminoalkyl, substituted or unsubstituted             C₃-C₆cycloalkyl, substituted or unsubstituted             C₁-C₈alkylC₃-C₆cycloalkyl, substituted or unsubstituted             aryl, substituted or unsubstituted C₂-C₈heterocycloalkyl,             substituted or unsubstituted heteroaryl, C₁-C₄alkyl(aryl),             C₁-C₄alkyl(heteroaryl), C₁-C₈alkylethers, C₁-C₈alkylamides,             or C₁-C₄alkyl(C₂-C₈heterocycloalkyl); or     -   R₇ and R₈ taken together form a bond;         -   R₆ is H, substituted or unsubstituted C₁-C₄alkyl,             substituted or unsubstituted C₁-C₄heteroalkyl,             C₁-C₈alkylaminoalkyl, C₁-C₈hydroxyalkylaminoalkyl,             C₁-C₈alkoxyalkylaminoalkyl, substituted or unsubstituted             C₃-C₆cycloalkyl, substituted or unsubstituted             C₁-C₈alkylC₃-C₆cycloalkyl, substituted or unsubstituted             aryl, substituted or unsubstituted C₂-C₈heterocycloalkyl,             substituted or unsubstituted heteroaryl, C₁-C₄alkyl(aryl),             C₁-C₄alkyl(heteroaryl), C₁-C₈alkylethers, C₁-C₈alkylamides,             or C₁-C₄alkyl(C₂-C₈heterocycloalkyl); and     -   pharmaceutically acceptable active metabolites, pharmaceutically         acceptable solvates, pharmaceutically acceptable salts, or         pharmaceutically acceptable prodrugs thereof.

In a further or alternative embodiment, the “G” group of any of Formula (A1), Formula (B1), or Formula (C1) is any group that is used to tailor the physical and biological properties of the molecule. Such tailoring/modifications are achieved using groups which modulate Michael acceptor chemical reactivity, acidity, basicity, lipophilicity, solubility and other physical properties of the molecule. The physical and biological properties modulated by such modifications to G include, by way of example only, enhancing chemical reactivity of Michael acceptor group, solubility, in vivo absorption, and in vivo metabolism. In addition, in vivo metabolism includes, by way of example only, controlling in vivo PK properties, off-target activities, potential toxicities associated with cypP450 interactions, drug-drug interactions, and the like. Further, modifications to G allow for the tailoring of the in vivo efficacy of the compound through the modulation of, by way of example, specific and non-specific protein binding to plasma proteins and lipids and tissue distribution in vivo.

In one aspect are compounds (including irreversible inhibitors of ACKs, including Btk and its cysteine homologs) having the structure of Formula (D1):

wherein

-   -   L_(a) is CH₂, O, NH or S;     -   Ar is an optionally substituted aromatic carbocycle or an         aromatic heterocycle;     -   Y is an optionally substituted group selected from among         alkylene, heteroalkylene, arylene, heteroarylene,         alkylenearylene, alkyleneheteroarylene, and         alkyleneheterocycloalkylene, or combination thereof;     -   Z is C(═O), NHC(═O), NR^(a)C(═O), NR^(a)S(═O)_(x), where x is 1         or 2, and R^(a) is H, substituted or unsubstituted alkyl,         substituted or unsubstituted cycloalkyl; and either     -   R₇ and R₈ are H;         -   R₆ is H, substituted or unsubstituted C₁-C₄alkyl,             substituted or unsubstituted C₁-C₄heteroalkyl,             C₁-C₈alkylaminoalkyl, C₁-C₈hydroxyalkylaminoalkyl,             C₁-C₈alkoxyalkylaminoalkyl, substituted or unsubstituted             C₃-C₆cycloalkyl, substituted or unsubstituted             C₁-C₈alkylC₃-C₆cycloalkyl, substituted or unsubstituted             aryl, substituted or unsubstituted C₂-C₈heterocycloalkyl,             substituted or unsubstituted heteroaryl, C₁-C₄alkyl(aryl),             C₁-C₄alkyl(heteroaryl), C₁-C₈alkylethers, C₁-C₈alkylamides,             or C₁-C₄alkyl(C₂-C₈heterocycloalkyl);     -   R₆ and R₈ are H;         -   R₇ is H, substituted or unsubstituted C₁-C₄alkyl,             substituted or unsubstituted C₁-C₄heteroalkyl,             C₁-C₈alkylaminoalkyl, C₁-C₈hydroxyalkylaminoalkyl,             C₁-C₈alkoxyalkylaminoalkyl, substituted or unsubstituted             C₃-C₆cycloalkyl, substituted or unsubstituted             C₁-C₈alkylC₃-C₆cycloalkyl, substituted or unsubstituted             aryl, substituted or unsubstituted C₂-C₈heterocycloalkyl,             substituted or unsubstituted heteroaryl, C₁-C₄alkyl(aryl),             C₁-C₄alkyl(heteroaryl), C₁-C₈alkylethers, C₁-C₈alkylamides,             or C₁-C₄alkyl(C₂-C₈heterocycloalkyl); or     -   R₇ and R₈ taken together form a bond;         -   R₆ is H, substituted or unsubstituted C₁-C₄alkyl,             substituted or unsubstituted C₁-C₄heteroalkyl,             C₁-C₈alkylaminoalkyl, C₁-C₈hydroxyalkylaminoalkyl,             C₁-C₈alkoxyalkylaminoalkyl, substituted or unsubstituted             C₃-C₆cycloalkyl, substituted or unsubstituted             C₁-C₈alkylC₃-C₆cycloalkyl, substituted or unsubstituted             aryl, substituted or unsubstituted C₂-C₈heterocycloalkyl,             substituted or unsubstituted heteroaryl, C₁-C₄alkyl(aryl),             C₁-C₄alkyl(heteroaryl), C₁-C₈alkylethers, C₁-C₈alkylamides,             or C₁-C₄alkyl(C₂-C₈heterocycloalkyl);     -   or combinations thereof; and         pharmaceutically active metabolites, or pharmaceutically         acceptable solvates, pharmaceutically acceptable salts, or         pharmaceutically acceptable prodrugs thereof.

In another embodiment are provided pharmaceutically acceptable salts of compounds of Formula (D1). By way of example only, are salts of an amino group formed with inorganic acids such as hydrochloric acid, hydrobromic acid, phosphoric acid, sulfuric acid and perchloric acid or with organic acids such as acetic acid, oxalic acid, maleic acid, tartaric acid, citric acid, succinic acid or malonic acid. Further salts include those in which the counterion is an anion, such as adipate, alginate, ascorbate, aspartate, benzenesulfonate, benzoate, bisulfate, borate, butyrate, camphorate, camphorsulfonate, citrate, cyclopentanepropionate, digluconate, dodecylsulfate, ethanesulfonate, formate, fumarate, glucoheptonate, glycerophosphate, gluconate, hemisulfate, heptanoate, hexanoate, hydroiodide, 2-hydroxy-ethanesulfonate, lactobionate, lactate, laurate, lauryl sulfate, malate, maleate, malonate, methanesulfonate, 2-naphthalenesulfonate, nicotinate, nitrate, oleate, oxalate, palmitate, pamoate, pectinate, persulfate, 3-phenylpropionate, phosphate, picrate, pivalate, propionate, stearate, succinate, sulfate, tartrate, thiocyanate, p-toluenesulfonate, undecanoate, and valerate. Further salts include those in which the counterion is an cation, such as sodium, lithium, potassium, calcium, magnesium, ammonium, and quaternary ammonium (substituted with at least one organic moiety) cations.

In another embodiment are pharmaceutically acceptable esters of compounds of Formula (D1), including those in which the ester group is selected from a formate, acetate, propionate, butyrate, acrylate and ethylsuccinate.

In another embodiment are pharmaceutically acceptable carbamates of compounds of Formula (D1). In another embodiment are pharmaceutically acceptable N-acyl derivatives of compounds of Formula (D1). Examples of N-acyl groups include N-acetyl and N-ethoxycarbonyl groups.

In a further or alternative embodiment, L_(a) is O.

In a further or alternative embodiment, Ar is phenyl.

In a further or alternative embodiment, Z is C(═O), NHC(═O), or NCH₃C(═O).

In a further or alternative embodiment, each of R₁, R₂, and R₃ is H.

In one aspect are compounds (including irreversible inhibitors of ACKs, including Btk and its cysteine homologs) having the structure of Formula (D1):

wherein:

-   -   L_(a) is CH₂, O, NH or S;     -   Ar is a substituted or unsubstituted aryl, or a substituted or         unsubstituted heteroaryl;     -   Y is an optionally substituted group selected from among         alkylene, heteroalkylene, arylene, heteroarylene,         alkylenearylene, alkylenehetroarylene, alkylenecycloalkylene and         alkyleneheterocycloalkylene;     -   Z is C(═O), NHC(═O), NR^(a)C(═O), NR^(a)S(═O), where x is 1 or         2, and R^(a) is substituted or unsubstituted alkyl, substituted         or unsubstituted cycloalkyl; and either     -   R₇ and R₈ are H;         -   R₆ is H, substituted or unsubstituted C₁-C₄alkyl,             substituted or unsubstituted C₁-C₄heteroalkyl,             C₁-C₈alkylaminoalkyl, C₁-C₈hydroxyalkylaminoalkyl,             C₁-C₈alkoxyalkylaminoalkyl, substituted or unsubstituted             C₃-C₆cycloalkyl, substituted or unsubstituted             C₁-C₈alkylC₃-C₆cycloalkyl, substituted or unsubstituted             aryl, substituted or unsubstituted C₂-C₈heterocycloalkyl,             substituted or unsubstituted heteroaryl, C₁-C₄alkyl(aryl),             C₁-C₄alkyl(heteroaryl), C₁-C₈alkylethers, C₁-C₈alkylamides,             or C₁-C₄alkyl(C₂-C₈heterocycloalkyl);     -   R₆ and R₈ are H;         -   R₇ is H, substituted or unsubstituted C₁-C₄alkyl,             substituted or unsubstituted C₁-C₄heteroalkyl,             C₁-C₈alkylaminoalkyl, C₁-C₈hydroxyalkylaminoalkyl,             C₁-C₈alkoxyalkylaminoalkyl, substituted or unsubstituted             C₃-C₆cycloalkyl, substituted or unsubstituted             C₁-C₈alkylC₃-C₆cycloalkyl, substituted or unsubstituted             aryl, substituted or unsubstituted C₂-C₈heterocycloalkyl,             substituted or unsubstituted heteroaryl, C₁-C₄alkyl(aryl),             C₁-C₄alkyl(heteroaryl), C₁-C₈alkylethers, C₁-C₈alkylamides,             or C₁-C₄alkyl(C₂-C₈heterocycloalkyl); or     -   R₇ and R₈ taken together form a bond;         -   R₆ is H, substituted or unsubstituted C₁-C₄alkyl,             substituted or unsubstituted C₁-C₄heteroalkyl,             C₁-C₈alkylaminoalkyl, C₁-C₈hydroxyalkylaminoalkyl,             C₁-C₈alkoxyalkylaminoalkyl, substituted or unsubstituted             C₃-C₆cycloalkyl, substituted or unsubstituted             C₁-C₈alkylC₃-C₆cycloalkyl, substituted or unsubstituted             aryl, substituted or unsubstituted C₂-C₈heterocycloalkyl,             substituted or unsubstituted heteroaryl, C₁-C₄alkyl(aryl),             C₁-C₄alkyl(heteroaryl), C₁-C₈alkylethers, C₁-C₈alkylamides,             or C₁-C₄alkyl(C₂-C₈heterocycloalkyl); and             pharmaceutically active metabolites, or pharmaceutically             acceptable solvates, pharmaceutically acceptable salts, or             pharmaceutically acceptable prodrugs thereof.

In another embodiment are provided pharmaceutically acceptable salts of compounds of Formula (D1). By way of example only, are salts of an amino group formed with inorganic acids such as hydrochloric acid, hydrobromic acid, phosphoric acid, sulfuric acid and perchloric acid or with organic acids such as acetic acid, oxalic acid, maleic acid, tartaric acid, citric acid, succinic acid or malonic acid. Further salts include those in which the counterion is an anion, such as adipate, alginate, ascorbate, aspartate, benzenesulfonate, benzoate, bisulfate, borate, butyrate, camphorate, camphorsulfonate, citrate, cyclopentanepropionate, digluconate, dodecylsulfate, ethanesulfonate, formate, fumarate, glucoheptonate, glycerophosphate, gluconate, hemisulfate, heptanoate, hexanoate, hydroiodide, 2-hydroxy-ethanesulfonate, lactobionate, lactate, laurate, lauryl sulfate, malate, maleate, malonate, methanesulfonate, 2-naphthalenesulfonate, nicotinate, nitrate, oleate, oxalate, palmitate, pamoate, pectinate, persulfate, 3-phenylpropionate, phosphate, picrate, pivalate, propionate, stearate, succinate, sulfate, tartrate, thiocyanate, p-toluenesulfonate, undecanoate, and valerate. Further salts include those in which the counterion is an cation, such as sodium, lithium, potassium, calcium, magnesium, ammonium, and quaternary ammonium (substituted with at least one organic moiety) cations.

In another embodiment are pharmaceutically acceptable esters of compounds of Formula (D1), including those in which the ester group is selected from a formate, acetate, propionate, butyrate, acrylate and ethylsuccinate.

In another embodiment are pharmaceutically acceptable carbamates of compounds of Formula (D1). In another embodiment are pharmaceutically acceptable N-acyl derivatives of compounds of Formula (D1). Examples of N-acyl groups include N-acetyl and N-ethoxycarbonyl groups.

For any and all of the embodiments, substituents can be selected from among from a subset of the listed alternatives. For example, in some embodiments, L_(a) is CH₂, O, or NH. In other embodiments, L_(a) is O or NH. In yet other embodiments, L_(a) is O.

In some embodiments, Ar is a substituted or unsubstituted aryl. In yet other embodiments, Ar is a 6-membered aryl. In some other embodiments, Ar is phenyl.

In some embodiments, x is 2. In yet other embodiments, Z is C(═O), OC(═O), NHC(═O), S(═O)_(x), OS(═O)_(x), or NHS(═O)_(x). In some other embodiments, Z is C(═O), NHC(═O), or S(═O)₂.

In some embodiments, R₇ and R₈ are independently selected from among H, unsubstituted C₁-C₄ alkyl, substituted C₁-C₄alkyl, unsubstituted C₁-C₄heteroalkyl, and substituted C₁-C₄heteroalkyl; or R₇ and R₈ taken together form a bond. In yet other embodiments, each of R₇ and R₈ is H; or R₇ and R₈ taken together form a bond.

In some embodiments, R₆ is H, substituted or unsubstituted C₁-C₄alkyl, substituted or unsubstituted C₁-C₄heteroalkyl, C₁-C₆alkoxyalkyl, C₁-C₂alkyl-N(C₁-C₃alkyl)₂, substituted or unsubstituted aryl, substituted or unsubstituted heteroaryl, C₁-C₄alkyl(aryl), C₁-C₄alkyl(heteroaryl), C₁-C₄alkyl(C₃-C₈cycloalkyl), or C₁-C₄alkyl(C₂-C₈heterocycloalkyl). In some other embodiments, R₆ is H, substituted or unsubstituted C₁-C₄alkyl, substituted or unsubstituted C₁-C₄heteroalkyl, C₁-C₆alkoxyalkyl, C₁-C₂alkyl-N(C₁-C₃alkyl)₂, C₁-C₄alkyl(aryl), C₁-C₄alkyl(heteroaryl), C₁-C₄alkyl(C₃-C₈cycloalkyl), or C₁-C₄alkyl(C₂-C₈heterocycloalkyl). In yet other embodiments, R₆ is H, substituted or unsubstituted C₁-C₄alkyl, —CH₂—O—(C₁-C₃alkyl), —CH₂—N(C₁-C₃alkyl)₂, C₁-C₄alkyl(phenyl), or C₁-C₄alkyl(5- or 6-membered heteroaryl). In some embodiments, R₆ is H, substituted or unsubstituted C₁-C₄alkyl, —CH₂—O—(C₁-C₃alkyl), —CH₂—N(C₁-C₃alkyl)₂, C₁-C₄alkyl(phenyl), or C₁-C₄alkyl(5- or 6-membered heteroaryl containing 1 or 2 N atoms), or C₁-C₄alkyl(5- or 6-membered heterocycloalkyl containing 1 or 2 N atoms).

In some embodiments, Y is an optionally substituted group selected from among alkylene, heteroalkylene, cycloalkylene, and heterocycloalkylene. In other embodiments, Y is an optionally substituted group selected from among C₁-C₆alkylene, C₁-C₆heteroalkylene, 4-, 5-, 6- or 7-membered cycloalkylene, and 4-, 5-, 6- or 7-membered heterocycloalkylene. In yet other embodiments, Y is an optionally substituted group selected from among C₁-C₆alkylene, C₁-C₆heteroalkylene, 5-, or 6-membered cycloalkylene, and 5-, or 6-membered heterocycloalkylene containing 1 or 2 N atoms. In some other embodiments, Y is a 5-, or 6-membered cycloalkylene, or a 5-, or 6-membered heterocycloalkylene containing 1 or 2 N atoms.

In one aspect are compounds (including irreversible inhibitors of ACKs, including Btk and its cysteine homologs) having the structure of Formula (A2-A6):

wherein

-   -   R₁ is H, L₂-(substituted or unsubstituted alkyl),         L₂-(substituted or unsubstituted cycloalkyl), L₂-(substituted or         unsubstituted alkenyl), L₂-(substituted or unsubstituted         cycloalkenyl), L₂-(substituted or unsubstituted heterocycle),         L₂-(substituted or unsubstituted heteroaryl), or L₂-(substituted         or unsubstituted aryl), where L₂ is a bond, O, S, —S(═O),         —S(═O)₂, C(═O), -(substituted or unsubstituted C₁-C₆ alkylene),         or -(substituted or unsubstituted C₂-C₆ alkenylene);     -   R₂ and R₃ are independently selected from H, lower alkyl and         substituted lower alkyl;     -   R₄ is L₃-X-L₄-G, wherein,         -   L₃ is optional, and when present is a bond, optionally             substituted or unsubstituted alkylene, optionally             substituted or unsubstituted cycloalkylene, optionally             substituted or unsubstituted alkenylene, optionally             substituted or unsubstituted alkynylene;         -   X is optional, and when present is a bond, O, —C(═O), S,             —S(═O), —S(═O)₂, —NH, —NR₉, —NHC(O), —C(O)NH, —NR₉C(O),             —C(O)NR₉, —S(═O)₂NH, —NHS(═O)₂, —S(═O)₂NR₉—, —NR₉S(═O)₂,             —OC(O)NH—, —NHC(O)O—, —OC(O)NR₉—, —NR₉C(O)O—, —CH═NO—,             —ON═CH—, —NR₁₀C(O)NR₁₀—, heteroarylene, arylene,             —NR₁₀C(═NR₁₁)NR₁₀—, —NR₁₀C(═NR₁₁)—, —C(═NR₁₁)NR₁₀—,             —OC(═NR₁₁)—, or —C(═NR₁₁)O—;         -   L₄ is optional, and when present is a bond, substituted or             unsubstituted alkylene, substituted or unsubstituted             cycloalkylene, substituted or unsubstituted alkenylene,             substituted or unsubstituted alkynylene, substituted or             unsubstituted arylene, substituted or unsubstituted             heteroarylene, substituted or unsubstituted heterocyclene;         -   or L₃, X and L₄ taken together form a nitrogen containing             heterocyclic ring;         -   G is

-   -    wherein,         -   R₆, R₇ and R₈ are independently selected from among H, lower             alkyl or substituted lower alkyl, lower heteroalkyl or             substituted lower heteroalkyl, substituted or unsubstituted             lower cycloalkyl, and substituted or unsubstituted lower             heterocycloalkyl;     -   R₉ is selected from among H, substituted or unsubstituted lower         alkyl, and substituted or unsubstituted lower cycloalkyl;     -   each R₁₀ is independently H, substituted or unsubstituted lower         alkyl, or substituted or unsubstituted lower cycloalkyl; or     -   two R₁₀ groups can together form a 5-, 6-, 7-, or 8-membered         heterocyclic ring; or     -   R₁₀ and R₁₁ can together form a 5-, 6-, 7-, or 8-membered         heterocyclic ring; or     -   R₁₁ is selected from H, —S(═O)₂R₈, —S(═O)₂NH₂, —C(O)R₈, —CN,         —NO₂, heteroaryl, or heteroalkyl; and         pharmaceutically active metabolites, or pharmaceutically         acceptable solvates, pharmaceutically acceptable salts, or         pharmaceutically acceptable prodrugs thereof.

In another embodiment are provided pharmaceutically acceptable salts of compounds of Formula (A2-A6). By way of example only, are salts of an amino group formed with inorganic acids such as hydrochloric acid, hydrobromic acid, phosphoric acid, sulfuric acid and perchloric acid or with organic acids such as acetic acid, oxalic acid, maleic acid, tartaric acid, citric acid, succinic acid or malonic acid. Further salts include those in which the counterion is an anion, such as adipate, alginate, ascorbate, aspartate, benzenesulfonate, benzoate, bisulfate, borate, butyrate, camphorate, camphorsulfonate, citrate, cyclopentanepropionate, digluconate, dodecylsulfate, ethanesulfonate, formate, fumarate, glucoheptonate, glycerophosphate, gluconate, hemisulfate, heptanoate, hexanoate, hydroiodide, 2-hydroxy-ethanesulfonate, lactobionate, lactate, laurate, lauryl sulfate, malate, maleate, malonate, methanesulfonate, 2-naphthalenesulfonate, nicotinate, nitrate, oleate, oxalate, palmitate, pamoate, pectinate, persulfate, 3-phenylpropionate, phosphate, picrate, pivalate, propionate, stearate, succinate, sulfate, tartrate, thiocyanate, p-toluenesulfonate, undecanoate, and valerate. Further salts include those in which the counterion is an cation, such as sodium, lithium, potassium, calcium, magnesium, ammonium, and quaternary ammonium (substituted with at least one organic moiety) cations.

In another embodiment are pharmaceutically acceptable esters of compounds of Formula (A2-A6), including those in which the ester group is selected from a formate, acetate, propionate, butyrate, acrylate and ethylsuccinate.

In another embodiment are pharmaceutically acceptable carbamates of compounds of Formula (A2-A6). In another embodiment are pharmaceutically acceptable N-acyl derivatives of compounds of Formula (A2-A6). Examples of N-acyl groups include N-acetyl and N-ethoxycarbonyl groups.

In a further or alternative embodiment, the compound of Formula (A2-A6) has the following structure of Formula (B2-B6):

wherein:

-   -   Y is alkylene or substituted alkylene, or a 4-, 5-, or         6-membered cycloalkylene ring;     -   each R_(a) is independently H, halogen, —CF₃, —CN, —NO₂, OH,         NH₂, -L_(a)-(substituted or unsubstituted alkyl),         -L_(a)-(substituted or unsubstituted alkenyl),         -L_(a)-(substituted or unsubstituted heteroaryl), or         -L_(a)-(substituted or unsubstituted aryl), wherein L_(a) is a         bond, O, S, —S(═O), —S(═O)₂, NH, C(O), CH₂, —NHC(O)O, —NHC(O),         or —C(O)NH;     -   G is

-   -    wherein,     -   R₆, R₇ and R₈ are independently selected from among H, lower         alkyl or substituted lower alkyl, lower heteroalkyl or         substituted lower heteroalkyl, substituted or unsubstituted         lower cycloalkyl, and substituted or unsubstituted lower         heterocycloalkyl;     -   R₁₂ is H or lower alkyl; or     -   Y and R₁₂ taken together form a 4-, 5-, or 6-membered         heterocyclic ring; and     -   pharmaceutically acceptable active metabolites, pharmaceutically         acceptable solvates, pharmaceutically acceptable salts, or         pharmaceutically acceptable prodrugs thereof.

In further or alternative embodiments, G is selected from among

In further or alternative embodiments,

is selected from among

In further or alternative embodiment, the compound of Formula (B2-B6) has the following structure of Formula (C2-C6):

-   -   Y is alkylene or substituted alkylene, or a 4-, 5-, or         6-membered cycloalkylene ring;     -   R₁₂ is H or lower alkyl; or     -   Y and R₁₂ taken together form a 4-, 5-, or 6-membered         heterocyclic ring;     -   G is

-   -    wherein,     -   R₆, R₇ and R₈ are independently selected from among H, lower         alkyl or substituted lower alkyl, lower heteroalkyl or         substituted lower heteroalkyl, substituted or unsubstituted         lower cycloalkyl, and substituted or unsubstituted lower         heterocycloalkyl; and     -   pharmaceutically acceptable active metabolites, pharmaceutically         acceptable solvates, pharmaceutically acceptable salts, or         pharmaceutically acceptable prodrugs thereof.

In a further or alternative embodiment, the “G” group of any of Formula (A2-A6), Formula (B2-B6), or Formula (C2-C6) is any group that is used to tailor the physical and biological properties of the molecule. Such tailoring/modifications are achieved using groups which modulate Michael acceptor chemical reactivity, acidity, basicity, lipophilicity, solubility and other physical properties of the molecule. The physical and biological properties modulated by such modifications to G include, by way of example only, enhancing chemical reactivity of Michael acceptor group, solubility, in vivo absorption, and in vivo metabolism. In addition, in vivo metabolism includes, by way of example only, controlling in vivo PK properties, off-target activities, potential toxicities associated with cypP450 interactions, drug-drug interactions, and the like. Further, modifications to G allow for the tailoring of the in vivo efficacy of the compound through the modulation of, by way of example, specific and non-specific protein binding to plasma proteins and lipids and tissue distribution in vivo.

In some embodiments, the compound is AVL-263 (Avila Therapeutics/Celgene Corporation), AVL-292 (Avila Therapeutics/Celgene Corporation), AVL-291 (Avila Therapeutics/Celgene Corporation), BMS-488516 (Bristol-Myers Squibb), BMS-509744 (Bristol-Myers Squibb), CGI-1746 (CGI Pharma/Gilead Sciences), CTA-056, GDC-0834 (Genentech), GDC-0853 (Genentech), HY-11066 (also, CTK4I7891, HMS3265G21, HMS3265G22, HMS3265H21, HMS3265H22, 439574-61-5, AG-F-54930), ACP-196, ONO-4059 (Ono Pharmaceutical Co., Ltd.), ONO-WG37 (Ono Pharmaceutical Co., Ltd.), PLS-123 (Peking University), RN486 (Hoffmann-La Roche), or HM71224 (Hanmi Pharmaceutical Company Limited).

In some embodiments, the compound is 4-(tert-butyl)-N-(2-methyl-3-(4-methyl-6-((4-(morpholine-4-carbonyl)phenyl)amino)-5-oxo-4,5-dihydropyrazin-2-yl)phenyl)benzamide (CGI-1746); 7-benzyl-1-(3-(piperidin-1-yl)propyl)-2-(4-(pyridin-4-yl)phenyl)-1H-imidazo[4,5-g]quinoxalin-6(5H)-one (CTA-056); (R)—N-(3-(6-(4-(1,4-dimethyl-3-oxopiperazin-2-yl)phenylamino)-4-methyl-5-oxo-4,5-dihydropyrazin-2-yl)-2-methylphenyl)-4,5,6,7-tetrahydrobenzo[b]thiophene-2-carboxamide (GDC-0834); 6-cyclopropyl-8-fluoro-2-(2-hydroxymethyl-3-{1-methyl-5-[5-(4-methyl-piperazin-1-yl)-pyridin-2-ylamino]-6-oxo-1,6-dihydro-pyridin-3-yl}-phenyl)-2H-isoquinolin-1-one (RN-486); N-[5-[5-(4-acetylpiperazine-1-carbonyl)-4-methoxy-2-methylphenyl]sulfanyl-1,3-thiazol-2-yl]-4-[(3,3-dimethylbutan-2-ylamino)methyl]benzamide (BMS-509744, HY-11092); or N-(5-((5-(4-Acetylpiperazine-1-carbonyl)-4-methoxy-2-methylphenyl)thio)thiazol-2-yl)-4-(((3-methylbutan-2-yl)amino)methyl)benzamide (HY11066).

In other embodiments, the compound is:

In another embodiment are provided pharmaceutically acceptable salts of compounds of the compounds disclosed herein. By way of example only, are salts of an amino group formed with inorganic acids such as hydrochloric acid, hydrobromic acid, phosphoric acid, sulfuric acid and perchloric acid or with organic acids such as acetic acid, oxalic acid, maleic acid, tartaric acid, citric acid, succinic acid or malonic acid. Further salts include those in which the counterion is an anion, such as adipate, alginate, ascorbate, aspartate, benzenesulfonate, benzoate, bisulfate, borate, butyrate, camphorate, camphorsulfonate, citrate, cyclopentanepropionate, digluconate, dodecylsulfate, ethanesulfonate, formate, fumarate, glucoheptonate, glycerophosphate, gluconate, hemisulfate, heptanoate, hexanoate, hydroiodide, 2-hydroxy-ethanesulfonate, lactobionate, lactate, laurate, lauryl sulfate, malate, maleate, malonate, methanesulfonate, 2-naphthalenesulfonate, nicotinate, nitrate, oleate, oxalate, palmitate, pamoate, pectinate, persulfate, 3-phenylpropionate, phosphate, picrate, pivalate, propionate, stearate, succinate, sulfate, tartrate, thiocyanate, p-toluenesulfonate, undecanoate, and valerate. Further salts include those in which the counterion is an cation, such as sodium, lithium, potassium, calcium, magnesium, ammonium, and quaternary ammonium (substituted with at least one organic moiety) cations.

In one aspect are compounds (including irreversible inhibitors of ACKs, including Btk and its cysteine homologs) having the structure of Formula (D2-D6):

wherein:

-   -   L_(a) is CH₂, O, NH or S;     -   Ar is a substituted or unsubstituted aryl, or a substituted or         unsubstituted heteroaryl;     -   Y is an optionally substituted group selected from among         alkylene, heteroalkylene, cycloalkylene, heterocycloalkylene,         arylene, and heteroarylene;     -   Z is C(═O), OC(═O), NHC(═O), C(═S), S(═O)_(x), OS(═O)_(x),         NHS(═O)_(x), where x is 1 or 2;     -   R₇ and R₈ are independently selected from among H, unsubstituted         C₁-C₄alkyl, substituted C₁-C₄alkyl, unsubstituted         C₁-C₄heteroalkyl, substituted C₁-C₄heteroalkyl, unsubstituted         C₃-C₆cycloalkyl, substituted C₃-C₆cycloalkyl, unsubstituted         C₂-C₆heterocycloalkyl, and substituted C₂-C₆heterocycloalkyl; or     -   R₇ and R₈ taken together form a bond;     -   R₆ is H, substituted or unsubstituted C₁-C₄alkyl, substituted or         unsubstituted C₁-C₄heteroalkyl, C₁-C₆alkoxyalkyl,         C₁-C₈alkylaminoalkyl, substituted or unsubstituted         C₃-C₆cycloalkyl, substituted or unsubstituted aryl, substituted         or unsubstituted C₂-C₈heterocycloalkyl, substituted or         unsubstituted heteroaryl, C₁-C₄alkyl(aryl),         C₁-C₄alkyl(heteroaryl), C₁-C₄alkyl(C₃-C₈cycloalkyl), or         C₁-C₄alkyl(C₂-C₈heterocycloalkyl); and         pharmaceutically active metabolites, or pharmaceutically         acceptable solvates, pharmaceutically acceptable salts, or         pharmaceutically acceptable prodrugs thereof.

In another embodiment are provided pharmaceutically acceptable salts of compounds of Formula (D2-D6). By way of example only, are salts of an amino group formed with inorganic acids such as hydrochloric acid, hydrobromic acid, phosphoric acid, sulfuric acid and perchloric acid or with organic acids such as acetic acid, oxalic acid, maleic acid, tartaric acid, citric acid, succinic acid or malonic acid. Further salts include those in which the counterion is an anion, such as adipate, alginate, ascorbate, aspartate, benzenesulfonate, benzoate, bisulfate, borate, butyrate, camphorate, camphorsulfonate, citrate, cyclopentanepropionate, digluconate, dodecylsulfate, ethanesulfonate, formate, fumarate, glucoheptonate, glycerophosphate, gluconate, hemisulfate, heptanoate, hexanoate, hydroiodide, 2-hydroxy-ethanesulfonate, lactobionate, lactate, laurate, lauryl sulfate, malate, maleate, malonate, methanesulfonate, 2-naphthalenesulfonate, nicotinate, nitrate, oleate, oxalate, palmitate, pamoate, pectinate, persulfate, 3-phenylpropionate, phosphate, picrate, pivalate, propionate, stearate, succinate, sulfate, tartrate, thiocyanate, p-toluenesulfonate, undecanoate, and valerate. Further salts include those in which the counterion is an cation, such as sodium, lithium, potassium, calcium, magnesium, ammonium, and quaternary ammonium (substituted with at least one organic moiety) cations.

In another embodiment are pharmaceutically acceptable esters of compounds of Formula (D2-D6), including those in which the ester group is selected from a formate, acetate, propionate, butyrate, acrylate and ethylsuccinate.

In another embodiment are pharmaceutically acceptable carbamates of compounds of Formula (D2-D6). In another embodiment are pharmaceutically acceptable N-acyl derivatives of compounds of Formula (D2-D6). Examples of N-acyl groups include N-acetyl and N-ethoxycarbonyl groups.

For any and all of the embodiments, substituents can be selected from among from a subset of the listed alternatives. For example, in some embodiments, L_(a) is CH₂, O, or NH. In other embodiments, L_(a) is O or NH. In yet other embodiments, L_(a) is O.

In some embodiments, Ar is a substituted or unsubstituted aryl. In yet other embodiments, Ar is a 6-membered aryl. In some other embodiments, Ar is phenyl.

In some embodiments, x is 2. In yet other embodiments, Z is C(═O), OC(═O), NHC(═O), S(═O)_(x), OS(═O)_(x), or NHS(═O)_(x). In some other embodiments, Z is C(═O), NHC(═O), or S(═O)₂.

In some embodiments, R₇ and R₈ are independently selected from among H, unsubstituted C₁-C₄ alkyl, substituted C₁-C₄alkyl, unsubstituted C₁-C₄heteroalkyl, and substituted C₁-C₄heteroalkyl; or R₇ and R₈ taken together form a bond. In yet other embodiments, each of R₇ and R₈ is H; or R₇ and R₈ taken together form a bond.

In some embodiments, R₆ is H, substituted or unsubstituted C₁-C₄alkyl, substituted or unsubstituted C₁-C₄heteroalkyl, C₁-C₆alkoxyalkyl, C₁-C₂alkyl-N(C₁-C₃alkyl)₂, substituted or unsubstituted aryl, substituted or unsubstituted heteroaryl, C₁-C₄alkyl(aryl), C₁-C₄alkyl(heteroaryl), C₁-C₄alkyl(C₃-C₈cycloalkyl), or C₁-C₄alkyl(C₂-C₈heterocycloalkyl). In some other embodiments, R₆ is H, substituted or unsubstituted C₁-C₄alkyl, substituted or unsubstituted C₁-C₄heteroalkyl, C₁-C₆alkoxyalkyl, C₁-C₂alkyl-N(C₁-C₃alkyl)₂, C₁-C₄alkyl(aryl), C₁-C₄alkyl(heteroaryl), C₁-C₄alkyl(C₃-C₈cycloalkyl), or C₁-C₄alkyl(C₂-C₈heterocycloalkyl). In yet other embodiments, R₆ is H, substituted or unsubstituted C₁-C₄alkyl, —CH₂—O—(C₁-C₃alkyl), —CH₂—N(C₁-C₃alkyl)₂, C₁-C₄alkyl(phenyl), or C₁-C₄alkyl(5- or 6-membered heteroaryl). In some embodiments, R₆ is H, substituted or unsubstituted C₁-C₄alkyl, —CH₂—O—(C₁-C₃alkyl), —CH₂—N(C₁-C₃alkyl)₂, C₁-C₄alkyl(phenyl), or C₁-C₄alkyl(5- or 6-membered heteroaryl containing 1 or 2 N atoms), or C₁-C₄alkyl(5- or 6-membered heterocycloalkyl containing 1 or 2 N atoms).

In some embodiments, Y is an optionally substituted group selected from among alkylene, heteroalkylene, cycloalkylene, and heterocycloalkylene. In other embodiments, Y is an optionally substituted group selected from among C₁-C₆alkylene, C₁-C₆heteroalkylene, 4-, 5-, 6- or 7-membered cycloalkylene, and 4-, 5-, 6- or 7-membered heterocycloalkylene. In yet other embodiments, Y is an optionally substituted group selected from among C₁-C₆alkylene, C₁-C₆heteroalkylene, 5-, or 6-membered cycloalkylene, and 5-, or 6-membered heterocycloalkylene containing 1 or 2 N atoms. In some other embodiments, Y is a 5-, or 6-membered cycloalkylene, or a 5-, or 6-membered heterocycloalkylene containing 1 or 2 N atoms.

Any combination of the groups described above for the various variables is contemplated herein.

Preparation of Compounds

Compounds of any of Formula (A1-A6), Formula (B1-B6), Formula (C1-C6), Formula (D1-D6), Formula (I), or Formula (VII) are optionally synthesized using standard synthetic techniques or using such methods known in combination with methods described herein. In additions, solvents, temperatures and other reaction conditions are presented herein for illustration only, and not to limit the scope of the methods and compositions described herein. As a further guide the following synthetic methods may also be utilized.

The reactions are optionally employed in a linear sequence to provide the compounds described herein or used to synthesize fragments which are subsequently joined by the methods described herein and/or documented elsewhere.

Formation of Covalent Linkages by Reaction of an Electrophile with a Nucleophile

The compounds described herein can be modified using various electrophiles or nucleophiles to form new functional groups or substituents. Table 1 entitled “Examples of Covalent Linkages and Precursors Thereof” lists selected examples of covalent linkages and precursor functional groups which yield and can be used as guidance toward the variety of electrophiles and nucleophiles combinations available. Precursor functional groups are shown as electrophilic groups and nucleophilic groups.

TABLE 1 Examples of Covalent Linkages and Precursors Thereof Covalent Linkage Product Electrophile Nucleophile Carboxamides Activated esters amines/anilines Carboxamides acyl azides amines/anilines Carboxamides acyl halides amines/anilines Esters acyl halides alcohols/phenols Esters acyl nitriles alcohols/phenols Carboxamides acyl nitriles amines/anilines Imines Aldehydes amines/anilines Hydrazones aldehydes or ketones Hydrazines Oximes aldehydes or ketones Hydroxylamines Alkyl amines alkyl halides amines/anilines Esters alkyl halides carboxylic acids Thioethers alkyl halides Thiols Ethers alkyl halides alcohols/phenols Thioethers alkyl sulfonates Thiols Esters alkyl sulfonates carboxylic acids Ethers alkyl sulfonates alcohols/phenols Esters Anhydrides alcohols/phenols Carboxamides Anhydrides amines/anilines Thiophenols aryl halides Thiols Aryl amines aryl halides Amines Thioethers Azindines Thiols Boronate esters Boronates Glycols Carboxamides carboxylic acids amines/anilines Esters carboxylic acids Alcohols hydrazines Hydrazides carboxylic acids N-acylureas or Anhydrides carbodiimides carboxylic acids Esters diazoalkanes carboxylic acids Thioethers Epoxides Thiols Thioethers haloacetamides Thiols Ammotriazines halotriazines amines/anilines Triazinyl ethers halotriazines alcohols/phenols Amidines imido esters amines/anilines Ureas Isocyanates amines/anilines Urethanes Isocyanates alcohols/phenols Thioureas isothiocyanates amines/anilines Thioethers Maleimides Thiols Phosphite esters phosphoramidites Alcohols Silyl ethers silyl halides Alcohols Alkyl amines sulfonate esters amines/anilines Thioethers sulfonate esters Thiols Esters sulfonate esters carboxylic acids Ethers sulfonate esters Alcohols Sulfonamides sulfonyl halides amines/anilines Sulfonate esters sulfonyl halides phenols/alcohols Alkyl thiol α,β-unsaturated ester thiols Alkyl ethers α,β-unsaturated ester alcohols Alkyl amines α,β-unsaturated ester amines Alkyl thiol Vinyl sulfone thiols Alkyl ethers Vinyl sulfone alcohols Alkyl amines Vinyl sulfone amines Vinyl sulfide Propargyl amide thiol

Use of Protecting Groups

In the reactions described, it may be necessary to protect reactive functional groups, for example hydroxy, amino, imino, thio or carboxy groups, where these are desired in the final product, to avoid their unwanted participation in the reactions. Protecting groups are used to block some or all reactive moieties and prevent such groups from participating in chemical reactions until the protective group is removed. In one embodiment, each protective group be removable by a different means. Protective groups that are cleaved under totally disparate reaction conditions fulfill the requirement of differential removal. Protective groups can be removed by acid, base, and hydrogenolysis. Groups such as trityl, dimethoxytrityl, acetal and t-butyldimethylsilyl are acid labile and may be used to protect carboxy and hydroxy reactive moieties in the presence of amino groups protected with Cbz groups, which are removable by hydrogenolysis, and Fmoc groups, which are base labile. Carboxylic acid and hydroxy reactive moieties may be blocked with base labile groups such as, but not limited to, methyl, ethyl, and acetyl in the presence of amines blocked with acid labile groups such as t-butyl carbamate or with carbamates that are both acid and base stable but hydrolytically removable.

Carboxylic acid and hydroxy reactive moieties may also be blocked with hydrolytically removable protective groups such as the benzyl group, while amine groups capable of hydrogen bonding with acids may be blocked with base labile groups such as Fmoc. Carboxylic acid reactive moieties may be protected by conversion to simple ester compounds as exemplified herein, or they may be blocked with oxidatively-removable protective groups such as 2,4-dimethoxybenzyl, while co-existing amino groups may be blocked with fluoride labile silyl carbamates.

Allyl blocking groups are useful in then presence of acid- and base-protecting groups since the former are stable and can be subsequently removed by metal or pi-acid catalysts. For example, an allyl-blocked carboxylic acid can be deprotected with a Pd⁰-catalyzed reaction in the presence of acid labile t-butyl carbamate or base-labile acetate amine protecting groups. Yet another form of protecting group is a resin to which a compound or intermediate may be attached. As long as the residue is attached to the resin, that functional group is blocked and cannot react. Once released from the resin, the functional group is available to react.

Typically blocking/protecting groups may be selected from:

Other protecting groups, plus a detailed description of techniques applicable to the creation of protecting groups and their removal are described in Greene and Wuts, Protective Groups in Organic Synthesis, 3rd Ed., John Wiley & Sons, New York, N. Y., 1999, and Kocienski, Protective Groups, Thieme Verlag, New York, N. Y., 1994, which are incorporated herein by reference for such disclosure.

Synthesis of Compounds

In certain embodiments, provided herein are methods of making and methods of using tyrosine kinase inhibitor compounds described herein. In certain embodiments, compounds described herein can be synthesized using the following synthetic schemes. Compounds may be synthesized using methodologies analogous to those described below by the use of appropriate alternative starting materials.

Described herein are compounds that inhibit the activity of tyrosine kinase(s), such as Btk, and processes for their preparation. Also described herein are pharmaceutically acceptable salts, pharmaceutically acceptable solvates, pharmaceutically active metabolites and pharmaceutically acceptable prodrugs of such compounds. Pharmaceutical compositions that include at least one such compound or a pharmaceutically acceptable salt, pharmaceutically acceptable solvate, pharmaceutically active metabolite or pharmaceutically acceptable prodrug of such compound, are provided.

The starting material used for the synthesis of the compounds described herein is either synthesized or obtained from commercial sources, such as, but not limited to, Aldrich Chemical Co. (Milwaukee, Wis.), Bachem (Torrance, Calif.), or Sigma Chemical Co. (St. Louis, Mo.). The compounds described herein, and other related compounds having different substituents are optionally synthesized using techniques and materials, such as described, for example, in March, ADVANCED ORGANIC CHEMISTRY 4^(th) Ed., (Wiley 1992); Carey and Sundberg, ADVANCED ORGANIC CHEMISTRY 4^(th) Ed., Vols. A and B (Plenum 2000, 2001); Green and Wuts, PROTECTIVE GROUPS IN ORGANIC SYNTHESIS 3^(rd) Ed., (Wiley 1999); Fieser and Fieser's Reagents for Organic Synthesis, Volumes 1-17 (John Wiley and Sons, 1991); Rodd's Chemistry of Carbon Compounds, Volumes 1-5 and Supplementals (Elsevier Science Publishers, 1989); Organic Reactions, Volumes 1-40 (John Wiley and Sons, 1991); and Larock's Comprehensive Organic Transformations (VCH Publishers Inc., 1989). Other methods for the synthesis of compounds described herein may be found in International Patent Publication No. WO 01/01982901, Arnold et al. Bioorganic & Medicinal Chemistry Letters 10 (2000) 2167-2170; Burchat et al. Bioorganic & Medicinal Chemistry Letters 12 (2002) 1687-1690. As a guide the following synthetic methods may be utilized.

The products of the reactions are optionally isolated and purified, if desired, using conventional techniques, including, but not limited to, filtration, distillation, crystallization, chromatography and the like. Such materials are optionally characterized using conventional means, including physical constants and spectral data.

Compounds described herein are optionally prepared using the synthetic methods described herein as a single isomer or a mixture of isomers.

A non-limiting example of a synthetic approach towards the preparation of compounds of any of Formula (A1-A6), Formula (B1-B6), Formula (C1-C6), Formula (D1-D6), Formula (I), or Formula (VII) is shown in Scheme I.

Halogenation of commercially available 1H-pyrazolo[3,4-d]pyrimidin-4-amine provides an entry into the synthesis of compounds of Formula (A1-A6), (B1-B6), (C1-C6) and/or (D1-D6). In one embodiment, 1H-pyrazolo[3,4-d]pyrimidin-4-amine is treated with N-iodosuccinamide to give 3-iodo-1H-pyrazolo[3,4-d]pyrimidin-4-amine. Metal catalyzed cross coupling reactions are then carried out on 3-iodo-1H-pyrazolo[3,4-d]pyrimidin-4-amine. In one embodiment, palladium mediated cross-coupling of a suitably substituted phenyl boronic acid under basic conditions constructs intermediate 2. Intermediate 2 is coupled with N-Boc-3-hydroxypiperidine (as non-limiting example) via Mitsunobu reaction to give the Boc (tert-butyloxycarbonyl) protected intermediate 3. After deprotection with acid, coupling with, but not limited to, an acid chloride, such as, but not limited to, acryloyl chloride, completes the synthesis to give Compound 13.

A non-limiting example of a synthetic approach towards the preparation of compounds containing the imidazotriazine moiety, is

shown in Scheme II.

A non-limiting example of a synthetic approach towards the preparation of compounds containing any imidazopyrazine moiety,

is shown in Scheme III.

A non-limiting example of a synthetic approach towards the preparation of compounds containing the pyrrolopyrimidine moiety,

is shown in Scheme IV.

A non-limiting example of a synthetic approach towards the preparation of compounds containing the Azaindole moiety,

is shown in Scheme V.

A non-limiting example of a synthetic approach towards the preparation of compounds containing the pyrrolopyrimidine moiety,

is shown in Scheme VI.

Using the synthetic methods described herein, tyrosine kinase inhibitors as disclosed herein are obtained in good yields and purity. The compounds prepared by the methods disclosed herein are purified by conventional means, such as, for example, filtration, recrystallization, chromatography, distillation, and combinations thereof.

Any combination of the groups described above for the various variables is contemplated herein.

Further Forms of Compounds

Compounds disclosed herein have a structure of any of Formula (A1-A6), Formula (B1-B6), Formula (C1-C6), Formula (D1-D6), Formula (I), or Formula (VII). It is understood that when reference is made to compounds described herein, it is meant to include compounds of any of Formula (A1-A6), Formula (B1-B6), Formula (C1-C6), Formula (D1-D6), Formula (I), or Formula (VII), as well as to all of the specific compounds that fall within the scope of these generic formulae, unless otherwise indicated.

The compounds described herein may possess one or more stereocenters and each center may exist in the R or S configuration. The compounds presented herein include all diastereomeric, enantiomeric, and epimeric forms as well as the appropriate mixtures thereof. Stereoisomers may be obtained, if desired, by methods such as, for example, the separation of stereoisomers by chiral chromatographic columns.

Diasteromeric mixtures can be separated into their individual diastereomers on the basis of their physical chemical differences by methods known, for example, by chromatography and/or fractional crystallization. In one embodiment, enantiomers can be separated by chiral chromatographic columns. In other embodiments, enantiomers can be separated by converting the enantiomeric mixture into a diastereomeric mixture by reaction with an appropriate optically active compound (e.g., alcohol), separating the diastereomers and converting (e.g., hydrolyzing) the individual diastereomers to the corresponding pure enantiomers. All such isomers, including diastereomers, enantiomers, and mixtures thereof are considered as part of the compositions described herein.

The methods and formulations described herein include the use of N-oxides, crystalline forms (also known as polymorphs), or pharmaceutically acceptable salts of compounds described herein, as well as active metabolites of these compounds having the same type of activity. In some situations, compounds exist as tautomers. All tautomers are included within the scope of the compounds presented herein. In addition, the compounds described herein can exist in unsolvated as well as solvated forms with pharmaceutically acceptable solvents such as water, ethanol, and the like. The solvated forms of the compounds presented herein are also considered to be disclosed herein.

Compounds of any of Formula (A1-A6), Formula (B1-B6), Formula (C1-C6), Formula (D1-D6), Formula (I), or Formula (VII) in unoxidized form can be prepared from N-oxides of compounds of any of Formula (A1-A6), Formula (B1-B6), Formula (C1-C6), Formula (D1-D6), Formula (I), or Formula (VII) by treating with a reducing agent, such as, but not limited to, sulfur, sulfur dioxide, triphenyl phosphine, lithium borohydride, sodium borohydride, phosphorus trichloride, tribromide, or the like in a suitable inert organic solvent, such as, but not limited to, acetonitrile, ethanol, aqueous dioxane, or the like at 0 to 80° C.

In some embodiments, compounds described herein are prepared as prodrugs. A “prodrug” refers to an agent that is converted into the parent drug in vivo. Prodrugs are often useful because, in some situations, they may be easier to administer than the parent drug. They may, for instance, be bioavailable by oral administration whereas the parent is not. The prodrug may also have improved solubility in pharmaceutical compositions over the parent drug. An example, without limitation, of a prodrug is a compound described herein, which is administered as an ester (the “prodrug”) to facilitate transmittal across a cell membrane where water solubility is detrimental to mobility but which then is metabolically hydrolyzed to the carboxylic acid, the active entity, once inside the cell where water-solubility is beneficial. A further example of a prodrug is a short peptide (polyaminoacid) bonded to an acid group where the peptide is metabolized to reveal the active moiety. In certain embodiments, upon in vivo administration, a prodrug is chemically converted to the biologically, pharmaceutically or therapeutically active form of the compound. In certain embodiments, a prodrug is enzymatically metabolized by one or more steps or processes to the biologically, pharmaceutically or therapeutically active form of the compound. To produce a prodrug, a pharmaceutically active compound is modified such that the active compound will be regenerated upon in vivo administration. The prodrug can be designed to alter the metabolic stability or the transport characteristics of a drug, to mask side effects or toxicity, to improve the flavor of a drug or to alter other characteristics or properties of a drug. By virtue of knowledge of pharmacodynamic processes and drug metabolism in vivo, once a pharmaceutically active compound is known, prodrugs of compounds can be designed (if desired) (for examples of this procedure applied to other compounds, see, e.g., Nogrady (1985) Medicinal Chemistry A Biochemical Approach, Oxford University Press, New York, pages 388-392; Silverman (1992), The Organic Chemistry of Drug Design and Drug Action, Academic Press, Inc., San Diego, pages 352-401, Saulnier et al., (1994), Bioorganic and Medicinal Chemistry Letters, Vol. 4, p. 1985).

Prodrug forms of the herein described compounds, wherein the prodrug is metabolized in vivo to produce a derivative as set forth herein are included within the scope of the claims. In some cases, some of the compounds herein-described are prodrugs for another derivative or active compound.

Prodrugs are often useful because, in some situations, they are easier to administer than the parent drug. They are, for instance, bioavailable by oral administration whereas the parent is not. The prodrug optionally has improved solubility in pharmaceutical compositions over the parent drug. Prodrugs may be designed as reversible drug derivatives, for use as modifiers to enhance drug transport to site-specific tissues. In some embodiments, the design of a prodrug increases the effective water solubility. See, e.g., Fedorak et al., Am. J. Physiol., 269:G210-218 (1995); McLoed et al., Gastroenterol, 106:405-413 (1994); Hochhaus et al., Biomed. Chrom., 6:283-286 (1992); J. Larsen and H. Bundgaard, Int. J. Pharmaceutics, 37, 87 (1987); J. Larsen et al., Int. J. Pharmaceutics, 47, 103 (1988); Sinkula et al., J. Pharm. Sci., 64:181-210 (1975); T. Higuchi and V. Stella, Pro-drugs as Novel Delivery Systems, Vol. 14 of the A.C.S. Symposium Series; and Edward B. Roche, Bioreversible Carriers in Drug Design, American Pharmaceutical Association and Pergamon Press, 1987, all incorporated by reference for such disclosure.

Sites on the aromatic ring portion of compounds of any of Formula (A1-A6), Formula (B1-B6), Formula (C1-C6), Formula (D1-D6), Formula (I), or Formula (VII) can be susceptible to various metabolic reactions, therefore incorporation of appropriate substituents on the aromatic ring structures, such as, by way of example only, halogens can reduce, minimize or eliminate this metabolic pathway.

Compounds described herein include isotopically-labeled compounds, which are identical to those recited in the various formulas and structures presented herein, but for the fact that one or more atoms are replaced by an atom having an atomic mass or mass number different from the atomic mass or mass number usually found in nature. Examples of isotopes that can be incorporated into the present compounds include isotopes of hydrogen, carbon, nitrogen, oxygen, sulfur, fluorine and chlorine, such as ²H, ³H, ¹³C, ¹⁴C, ¹⁵N, ¹⁸O, ¹⁷O, ³⁵S, ¹⁸F, ³⁶Cl, respectively. Certain isotopically labeled compounds described herein, for example those into which radioactive isotopes such as ³H and ¹⁴C are incorporated, are useful in drug and/or substrate tissue distribution assays. Further, substitution with isotopes such as deuterium, i.e., ²H, can afford certain therapeutic advantages resulting from greater metabolic stability, for example increased in vivo half-life or reduced dosage requirements.

In additional or further embodiments, the compounds described herein are metabolized upon administration to an organism in need to produce a metabolite that is then used to produce a desired effect, including a desired therapeutic effect.

Compounds described herein (for example, compounds of any of Formula (A1-A6), Formula (B1-B6), Formula (C1-C6), Formula (D1-D6), Formula (I), or Formula (VII)) are optionally in the form of, and/or used as, pharmaceutically acceptable salts. The type of pharmaceutical acceptable salts, include, but are not limited to: (1) acid addition salts, formed) by reacting the free base form of the compound with a pharmaceutically acceptable: inorganic acid such as hydrochloric acid, hydrobromic acid, sulfuric acid, nitric acid, phosphoric acid, metaphosphoric acid, and the like; or with an organic acid such as acetic acid, propionic acid, hexanoic acid, cyclopentanepropionic acid, glycolic acid, pyruvic acid, lactic acid, malonic acid, succinic acid, malic acid, maleic acid, fumaric acid, trifluoroacetic acid, tartaric acid, citric acid, benzoic acid, 3-(4-hydroxybenzoyl)benzoic acid, cinnamic acid, mandelic acid, methanesulfonic acid, ethanesulfonic acid, 1,2-ethanedisulfonic acid, 2-hydroxyethanesulfonic acid, benzenesulfonic acid, toluenesulfonic acid, 2-naphthalenesulfonic acid, 4-methylbicyclo-[2.2.2]oct-2-ene-1-carboxylic acid, glucoheptonic acid, 4,4′-methylenebis-(3-hydroxy-2-ene-1-carboxylic acid), 3-phenylpropionic acid, trimethylacetic acid, tertiary butylacetic acid, lauryl sulfuric acid, gluconic acid, glutamic acid, hydroxynaphthoic acid, salicylic acid, stearic acid, muconic acid, and the like; (2) salts formed when an acidic proton present in the parent compound either is replaced by a metal ion, e.g., an alkali metal ion (e.g. lithium, sodium, potassium), an alkaline earth ion (e.g. magnesium, or calcium), or an aluminum ion; or coordinates with an organic base. Acceptable organic bases include ethanolamine, diethanolamine, triethanolamine, tromethamine, N-methylglucamine, and the like. Acceptable inorganic bases include aluminum hydroxide, calcium hydroxide, potassium hydroxide, sodium carbonate, sodium hydroxide, and the like.

The corresponding counterions of the pharmaceutically acceptable salts are optionally analyzed and identified using various methods including, but not limited to, ion exchange chromatography, ion chromatography, capillary electrophoresis, inductively coupled plasma, atomic absorption spectroscopy, mass spectrometry, or any combination thereof.

The salts are recovered by using at least one of the following techniques: filtration, precipitation with a non-solvent followed by filtration, evaporation of the solvent, or, in the case of aqueous solutions, lyophilization.

It should be understood that a reference to a pharmaceutically acceptable salt includes the solvent addition forms or crystal forms thereof, particularly solvates or polymorphs. Solvates contain either stoichiometric or non-stoichiometric amounts of a solvent, and are optionally formed during the process of crystallization with pharmaceutically acceptable solvents such as water, ethanol, and the like. Hydrates are formed when the solvent is water, or alcoholates are formed when the solvent is alcohol. Solvates of compounds described herein can be conveniently prepared or formed during the processes described herein. In addition, the compounds provided herein can exist in unsolvated as well as solvated forms. In general, the solvated forms are considered equivalent to the unsolvated forms for the purposes of the compounds and methods provided herein.

It should be understood that a reference to a salt includes the solvent addition forms or crystal forms thereof, particularly solvates or polymorphs. Solvates contain either stoichiometric or non-stoichiometric amounts of a solvent, and are often formed during the process of crystallization with pharmaceutically acceptable solvents such as water, ethanol, and the like. Hydrates are formed when the solvent is water, or alcoholates are formed when the solvent is alcohol. Polymorphs include the different crystal packing arrangements of the same elemental composition of a compound. Polymorphs usually have different X-ray diffraction patterns, infrared spectra, melting points, density, hardness, crystal shape, optical and electrical properties, stability, and solubility. Various factors such as the recrystallization solvent, rate of crystallization, and storage temperature may cause a single crystal form to dominate.

Compounds described herein are optionally in various forms, including but not limited to, amorphous forms, milled forms and nano-particulate forms. In addition, compounds described herein include crystalline forms, also known as polymorphs. Polymorphs include the different crystal packing arrangements of the same elemental composition of a compound. Polymorphs usually have different X-ray diffraction patterns, infrared spectra, melting points, density, hardness, crystal shape, optical and electrical properties, stability, and solubility. Various factors such as the recrystallization solvent, rate of crystallization, and storage temperature may cause a single crystal form to dominate.

The screening and characterization of the pharmaceutically acceptable salts, polymorphs and/or solvates may be accomplished using a variety of techniques including, but not limited to, thermal analysis, x-ray diffraction, spectroscopy, vapor sorption, and microscopy. Thermal analysis methods address thermo chemical degradation or thermo physical processes including, but not limited to, polymorphic transitions, and such methods are used to analyze the relationships between polymorphic forms, determine weight loss, to find the glass transition temperature, or for excipient compatibility studies. Such methods include, but are not limited to, Differential scanning calorimetry (DSC), Modulated Differential Scanning calorimetry (MDCS), Thermogravimetric analysis (TGA), and Thermogravi-metric and Infrared analysis (TG/IR). X-ray diffraction methods include, but are not limited to, single crystal and powder diffractometers and synchrotron sources. The various spectroscopic techniques used include, but are not limited to, Raman, FTIR, UVIS, and NMR (liquid and solid state). The various microscopy techniques include, but are not limited to, polarized light microscopy, Scanning Electron Microscopy (SEM) with Energy Dispersive X-Ray Analysis (EDX), Environmental Scanning Electron Microscopy with EDX (in gas or water vapor atmosphere), IR microscopy, and Raman microscopy.

Method for Detecting and Measuring a Btk Inhibitor Level in Human CNS Fluid

Described herein, in certain embodiments, are methods for detecting and measuring a Btk inhibitor level in human CNS fluid, comprising:

-   -   a. obtaining a cerebrospinal fluid (CSF) sample; and     -   b. measuring the level of the Btk inhibitor from the CSF sample         thereby determining the amount of the Btk inhibitor present in         the CNS fluid.

In some embodiments the measuring the level of the Btk inhibitor from the CSF sample is performed using liquid chromatography-tandem mass spectroscopy. In some embodiments the measuring the level of the Btk inhibitor from the CSF sample is performed using gas chromatography-tandem mass spectroscopy.

In some embodiments, the method further comprising centrifuging the CSF sample to obtain a supernatant portion and adding an internal standard to the supernatant portion of the CSF sample prior to analysis.

In some embodiments the method, further comprises:

-   -   a. integrating the area-under-the curve for a peak of the Btk         inhibitor from a plot of signal intensity as a function of         elution time from the liquid chromatography-tandem mass         spectroscopy;     -   b. integrating the area-under-the curve for a peak of the         internal standard from the plot of signal intensity as a         function of elution time from the liquid chromatography-tandem         mass spectroscopy;     -   c. determining a ratio by dividing the resultant integration         from step b by the resultant integration from step a;     -   d. providing a standard calibration curve; and     -   e. calculating the concentration of the Btk inhibitor in the CSF         sample by using a power fit regression formula without         weighting.

In some embodiments the slope and intercept are calculated from the standard calibration curve.

In some embodiments the Btk inhibitor is ibrutinib (PCI-32765). In some embodiments the Btk inhibitor is PCI-45227.

In some embodiments the internal standard for ibrutinib is d5-PCI-32765.

In some embodiments the internal standard for PCI-45227 is d5-PCI-45227.

In some embodiments the detection range of the Btk inhibitor in the CSF sample is from about 0.01 ng/mL to about 50 ng/mL. In some embodiments the detection range of the Btk inhibitor in the CSF sample is from about 0.1 ng/mL to about 20 ng/mL. In some embodiments the detection range of the Btk inhibitor in the CSF sample is from about 0.3 ng/mL to about 10 ng/mL.

In some embodiments the liquid chromatography is a high-performance liquid chromatography (HPLC).

In some embodiments the CSF sample is a stored CSF sample or a fresh CSF sample.

In some embodiments the stored CSF sample is a CSF sample stored on ice for at least 1 hour. In some embodiments the stored CSF sample is a CSF sample stored on ice for at least 2 hours. In some embodiments the stored CSF sample is a CSF sample stored on ice for at least 3 hours. In some embodiments the stored CSF sample is a CSF sample stored on ice for at least 4 hours.

In some embodiments the stored CSF sample is a CSF sample stored at −70±5° C. for at least 5 days. In some embodiments the stored CSF sample is a CSF sample stored at −70±5° C. for at least 6 days. In some embodiments the stored CSF sample is a CSF sample stored at −70±5° C. for at least 7 days. In some embodiments the stored CSF sample is a CSF sample stored at −70±5° C. for at least 8 days. In some embodiments the stored CSF sample is a CSF sample stored at −70±5° C. for at least 9 days.

In some embodiments the stored CSF sample is a CSF sample stored at −80±5° C. for at least 5 days. In some embodiments the stored CSF sample is a CSF sample stored at −80±5° C. for at least 6 days. In some embodiments the stored CSF sample is a CSF sample stored at −80±5° C. for at least 7 days. In some embodiments the stored CSF sample is a CSF sample stored at −80±5° C. for at least 8 days. In some embodiments the stored CSF sample is a CSF sample stored at −80±5° C. for at least 9 days.

In some embodiments the method further comprising processing a plasma sample to determine the concentration of the Btk inhibitor in the plasma sample, thereby providing an indication of the amount of the Btk inhibitor remaining in the plasma.

In some embodiments the detection range of the Btk inhibitor in the plasma sample is from about 1 ng/mL to about 1000 ng/mL.

Therapeutic Uses of Irreversible Inhibitor Compounds

Described herein are methods, compositions, uses and medicaments for the treatment of disorders characterized by the presence of a CNS malignancy comprising administering to an individual in need an irreversible inhibitor of an ACK. In some embodiments, the malignancy is a glioma or nonglioma. In some embodiments, the malignancy is a nonglioma. In other embodiments, the nongliomas include meningiomas, pituitary adenomas, primary CNS lymphomas, and medulloblastoma.

Also described herein are methods, compositions, uses and medicaments for the treatment of disorders characterized by the presence of a cancer that has metastasized into the CNS. In some cases, a cancer metastasized to CNS from another location is termed brain metastasis. In some embodiments, an ACK inhibitor is used to treat a brain metastasis. In some embodiments, the ACK inhibitor is a BTK inhibitor. In some embodiments, a BTK inhibitor is used to treat a brain metastasis. In some embodiments, the BTK inhibitor is ibrutinib. In some embodiments, ibrutinib is used to treat a brain metastasis. In some embodiments, a BTK inhibitor is used in combination with a second therapeutic agent to treat a brain metastasis. In some embodiments, ibrutinib is used in combination with a second therapeutic agent to treat a brain metastasis. In some embodiments, the cancer that has metastasized into the CNS is a solid tumor or a hematologic cancer. In some embodiments, the solid tumor is a sarcoma or carcinoma. In some embodiments, the hematologic cancer is a leukemia, a lymphoma, a myeloma, a non-Hodgkin's lymphoma, a Hodgkin's lymphoma, or a B-cell malignancy.

In some embodiments, an ACK inhibitor is used to treat a solid tumor that has metastasized into the CNS. In some embodiments, a BTK inhibitor is used to treat a solid tumor that has metastasized into the CNS. In some embodiments, ibrutinib is used to treat a solid tumor that has metastasized into the CNS.

In some embodiments, an ACK inhibitor is used to treat a hematologic cancer that has metastasized into the CNS. In some embodiments, a BTK inhibitor is used to treat a hematologic cancer that has metastasized into the CNS. In some embodiments, ibrutinib is used to treat a hematologic cancer that has metastasized into the CNS.

In some embodiments, exemplary sources of brain metastases includes, but is not limited to, breast cancer, lung cancer, ovarian cancer, prostate cancer, genitourinary tract cancers, osteosarcoma, leiomyosarcoma, milignant fibrous histiocytoma, alveolar soft part sarcoma, Ewing's bone sarcomas, melanoma, head and neck cancer, kidney, colorectal, pancreatic, neuroblastoma, chronic lymphocytic leukemia (CLL), acute lymphoblastic leukemia, acute myeloid leukemia, mantle cell lymphoma, diffuse large B-cell lymphoma (DLBCL), Burkitt's lymphoma, lymphoblastic lymphoma, follicular lymphoma, Waldenstrom's macroglobulinemia, myelocytic leukemia, enteropathy-type T-cell lymphoma, and peripheral T-cell lymphoma.

In some embodiments, an ACK inhibitor is used to treat a breast cancer, lung cancer, ovarian cancer, prostate cancer, genitourinary tract cancers, osteosarcoma, leiomyosarcoma, milignant fibrous histiocytoma, alveolar soft part sarcoma, Ewing's bone sarcomas, melanoma, head and neck cancer, kidney, colorectal, pancreatic, neuroblastoma, chronic lymphocytic leukemia (CLL), acute lymphoblastic leukemia, acute myeloid leukemia, mantle cell lymphoma, diffuse large B-cell lymphoma (DLBCL), Burkitt's lymphoma, lymphoblastic lymphoma, follicular lymphoma, Waldenstrom's macroglobulinemia, myelocytic leukemia, enteropathy-type T-cell lymphoma, and peripheral T-cell lymphoma that has metastasized into the CNS. In some embodiments, a BTK inhibitor is used to treat a breast cancer, lung cancer, ovarian cancer, prostate cancer, genitourinary tract cancers, osteosarcoma, leiomyosarcoma, milignant fibrous histiocytoma, alveolar soft part sarcoma, Ewing's bone sarcomas, melanoma, head and neck cancer, kidney, colorectal, pancreatic, neuroblastoma, chronic lymphocytic leukemia (CLL), acute lymphoblastic leukemia, acute myeloid leukemia, mantle cell lymphoma, diffuse large B-cell lymphoma (DLBCL), Burkitt's lymphoma, lymphoblastic lymphoma, follicular lymphoma, Waldenstrom's macroglobulinemia, myelocytic leukemia, enteropathy-type T-cell lymphoma, and peripheral T-cell lymphoma that has metastasized into the CNS. In some embodiments, ibrutininb is used to treat a breast cancer, lung cancer, ovarian cancer, prostate cancer, genitourinary tract cancers, osteosarcoma, leiomyosarcoma, milignant fibrous histiocytoma, alveolar soft part sarcoma, Ewing's bone sarcomas, melanoma, head and neck cancer, kidney, colorectal, pancreatic, neuroblastoma, chronic lymphocytic leukemia (CLL), acute lymphoblastic leukemia, acute myeloid leukemia, mantle cell lymphoma, diffuse large B-cell lymphoma (DLBCL), Burkitt's lymphoma, lymphoblastic lymphoma, follicular lymphoma, Waldenstrom's macroglobulinemia, myelocytic leukemia, enteropathy-type T-cell lymphoma, and peripheral T-cell lymphoma that has metastasized into the CNS.

In some embodiments, an ACK inhibitor is used to treat a breast cancer that has metastasized into the CNS. In some embodiments, a BTK inhibitor is used to treat a breast cancer that has metastasized into the CNS. In some embodiments, ibrutinib is used to treat a breast cancer that has metastasized into the CNS.

In some embodiments, breast cancer brain metastasis is correlated with a biomarker expression level. In some embodiments, the expression level is upregulated with respect to a reference level. In some embodiments, the expression level is down-regulated with respect to a reference level. Non-limiting examples of biomarkers include: ATAD2, DERL1, ESR1, CCND1, MYC, E2F1, NEK2A, CRYAB, HSPB2, FOXM1, DNMT3B, and MAT1A. In some embodiments, the expression levels of the biomarkers ATAD2, DERL1, ESR1, CCND1, MYC, E2F1, NEK2A, CRYAB, HSPB2, FOXM1, DNMT3B, and MAT1A are upregulated with respect to a reference level. In some embodiments, the expression levels of the biomarkers ATAD2, DERL1, ESR1, CCND1, MYC, E2F1, NEK2A, CRYAB, HSPB2, FOXM1, DNMT3B, and MAT1A are down-regulated with respect to a reference level.

In some embodiments, an ACK inhibitor is used to treat a lung cancer that has metastasized into the CNS. In some embodiments, a BTK inhibitor is used to treat a lung cancer that has metastasized into the CNS. In some embodiments, ibrutinib is used to treat a lung cancer that has metastasized into the CNS.

In some embodiments, lung cancer brain metastasis is correlated with a biomarker expression level. In some embodiments, the expression level is upregulated with respect to a reference level. In some embodiments, the expression level is down-regulated with respect to a reference level. Non-limiting examples of biomarkers include: SIRT1, KDM5B, CXCR4 and CXCL12. In some embodiments, the expression levels of the biomarkers SIRT1, KDM5B, CXCR4 and CXCL12 are upregulated with respect to a reference level. In some embodiments, the expression levels of the biomarkers SIRT1, KDM5B, CXCR4 and CXCL12 are down-regulated with respect to a reference level.

In some embodiments, an ACK inhibitor is used to treat a kidney cancer that has metastasized into the CNS. In some embodiments, a BTK inhibitor is used to treat a kidney cancer that has metastasized into the CNS. In some embodiments, ibrutinib is used to treat a kidney cancer that has metastasized into the CNS.

In some embodiments, an ACK inhibitor is used to treat a colorectal cancer that has metastasized into the CNS. In some embodiments, a BTK inhibitor is used to treat a colorectal cancer that has metastasized into the CNS. In some embodiments, ibrutinib is used to treat a colorectal cancer that has metastasized into the CNS.

In some embodiments, an ACK inhibitor is used to treat a pancreatic cancer that has metastasized into the CNS. In some embodiments, a BTK inhibitor is used to treat a pancreatic cancer that has metastasized into the CNS. In some embodiments, ibrutinib is used to treat a pancreatic cancer that has metastasized into the CNS.

In some embodiments, an ACK inhibitor is used to treat an ovarian cancer that has metastasized into the CNS. In some embodiments, a BTK inhibitor is used to treat an ovarian cancer that has metastasized into the CNS. In some embodiments, ibrutinib is used to treat an ovarian cancer that has metastasized into the CNS.

In some embodiments, an ACK inhibitor is used to treat a head and neck cancer that has metastasized into the CNS. In some embodiments, a BTK inhibitor is used to treat a head and neck cancer that has metastasized into the CNS. In some embodiments, ibrutinib is used to treat a head and neck cancer that has metastasized into the CNS.

In some embodiments, an ACK inhibitor is used to treat chronic lymphocytic leukemia (CLL) that has metastasized into the CNS. In some embodiments, a BTK inhibitor is used to treat chronic lymphocytic leukemia (CLL) that has metastasized into the CNS. In some embodiments, ibrutinib is used to treat chronic lymphocytic leukemia (CLL) that has metastasized into the CNS.

In some embodiments, an ACK inhibitor is used to treat acute lymphoblastic leukemia that has metastasized into the CNS. In some embodiments, a BTK inhibitor is used to treat acute lymphoblastic leukemia that has metastasized into the CNS. In some embodiments, ibrutinib is used to treat acute lymphoblastic leukemia that has metastasized into the CNS.

In some embodiments, an ACK inhibitor is used to treat acute myeloid leukemia that has metastasized into the CNS. In some embodiments, a BTK inhibitor is used to treat acute myeloid leukemia that has metastasized into the CNS. In some embodiments, ibrutinib is used to treat acute myeloid leukemia that has metastasized into the CNS.

In some embodiments, an ACK inhibitor is used to treat mantle cell lymphoma that has metastasized into the CNS. In some embodiments, a BTK inhibitor is used to treat mantle cell lymphoma that has metastasized into the CNS. In some embodiments, ibrutinib is used to treat mantle cell lymphoma that has metastasized into the CNS.

In some embodiments, an ACK inhibitor is used to treat diffuse large B-cell lymphoma (DLBCL) that has metastasized into the CNS. In some embodiments, a BTK inhibitor is used to treat diffuse large B-cell lymphoma (DLBCL) that has metastasized into the CNS. In some embodiments, ibrutinib is used to treat diffuse large B-cell lymphoma (DLBCL) that has metastasized into the CNS.

In some embodiments, an ACK inhibitor is used to treat Burkitt's lymphoma that has metastasized into the CNS. In some embodiments, a BTK inhibitor is used to treat Burkitt's lymphoma that has metastasized into the CNS. In some embodiments, ibrutinib is used to treat Burkitt's lymphoma that has metastasized into the CNS.

In some embodiments, an ACK inhibitor is used to treat lymphoblastic lymphoma that has metastasized into the CNS. In some embodiments, a BTK inhibitor is used to treat lymphoblastic lymphoma that has metastasized into the CNS. In some embodiments, ibrutinib is used to treat lymphoblastic lymphoma that has metastasized into the CNS.

In some embodiments, an ACK inhibitor is used to treat follicular lymphoma that has metastasized into the CNS. In some embodiments, a BTK inhibitor is used to treat follicular lymphoma that has metastasized into the CNS. In some embodiments, ibrutinib is used to treat follicular lymphoma that has metastasized into the CNS.

In some embodiments, an ACK inhibitor is used to treat Waldenstrom's macroglobulinemia that has metastasized into the CNS. In some embodiments, a BTK inhibitor is used to treat Waldenstrom's macroglobulinemia that has metastasized into the CNS. In some embodiments, ibrutinib is used to treat Waldenstrom's macroglobulinemia that has metastasized into the CNS.

In some embodiments, an ACK inhibitor is used to treat myelocytic leukemia that has metastasized into the CNS. In some embodiments, a BTK inhibitor is used to treat myelocytic leukemia that has metastasized into the CNS. In some embodiments, ibrutinib is used to treat myelocytic leukemia that has metastasized into the CNS.

In some embodiments, an ACK inhibitor is used to treat enteropathy-type T-cell lymphoma that has metastasized into the CNS. In some embodiments, a BTK inhibitor is used to treat enteropathy-type T-cell lymphoma that has metastasized into the CNS. In some embodiments, ibrutinib is used to treat enteropathy-type T-cell lymphoma that has metastasized into the CNS.

In some embodiments, an ACK inhibitor is used to treat peripheral T-cell lymphoma that has metastasized into the CNS. In some embodiments, a BTK inhibitor is used to treat peripheral T-cell lymphoma that has metastasized into the CNS. In some embodiments, ibrutinib is used to treat peripheral T-cell lymphoma that has metastasized into the CNS.

In some embodiments, an ACK inhibitor is used to treat an osteosarcoma that has metastasized into the CNS. In some embodiments, a BTK inhibitor is used to treat an osteosarcoma that has metastasized into the CNS. In some embodiments, ibrutinib is used to treat an osteosarcoma that has metastasized into the CNS.

In some embodiments, an ACK inhibitor is used to treat a melanoma that has metastasized into the CNS. In some embodiments, a BTK inhibitor is used to treat a melanoma that has metastasized into the CNS. In some embodiments, ibrutinib is used to treat a melanoma that has metastasized into the CNS.

In some embodiments, an ACK inhibitor is used to treat a neuroblastoma cancer that has metastasized into the CNS. In some embodiments, a BTK inhibitor is used to treat a neuroblastoma cancer that has metastasized into the CNS. In some embodiments, ibrutinib is used to treat a neuroblastoma cancer that has metastasized into the CNS.

In some embodiments, an ACK inhibitor is used to treat a lymphoma that has metastasized into the CNS. In some embodiments, a BTK inhibitor is used to treat a lymphoma that has metastasized into the CNS. In some embodiments, ibrutinib is used to treat a lymphoma that has metastasized into the CNS.

In some embodiments, an ACK inhibitor is used to treat a leiomyosarcoma cancer that has metastasized into the CNS. In some embodiments, a BTK inhibitor is used to treat a leiomyosarcoma cancer that has metastasized into the CNS. In some embodiments, ibrutinib is used to treat a leiomyosarcoma cancer that has metastasized into the CNS.

In some embodiments, an ACK inhibitor is used to treat a genitourinary tract cancer that has metastasized into the CNS. In some embodiments, a BTK inhibitor is used to treat a genitourinary tract cancer that has metastasized into the CNS. In some embodiments, ibrutinib is used to treat a genitourinary tract cancer that has metastasized into the CNS.

In some embodiments, an ACK inhibitor is used to treat a milignant fibrous histiocytoma that has metastasized into the CNS. In some embodiments, a BTK inhibitor is used to treat a milignant fibrous histiocytoma that has metastasized into the CNS. In some embodiments, ibrutinib is used to treat a milignant fibrous histiocytoma that has metastasized into the CNS.

In some embodiments, an ACK inhibitor is used to treat an alveolar soft part sarcoma that has metastasized into the CNS. In some embodiments, a BTK inhibitor is used to treat an alveolar soft part sarcoma that has metastasized into the CNS. In some embodiments, ibrutinib is used to treat an alveolar soft part sarcoma that has metastasized into the CNS.

In some embodiments, an ACK inhibitor is used to treat an Ewing's bone sarcomas that has metastasized into the CNS. In some embodiments, a BTK inhibitor is used to treat an Ewing's bone sarcomas that has metastasized into the CNS. In some embodiments, ibrutinib is used to treat an Ewing's bone sarcomas that has metastasized into the CNS.

As described herein, a sarcoma refers to a cancer of mesenchymal origin. Exemplary sarcoma includes, but is not limited to: alveolar rhabdomyosarcoma; alveolar soft part sarcoma; ameloblastoma; angiosarcoma; chondrosarcoma; chordoma; clear cell sarcoma of soft tissue; dedifferentiated liposarcoma; desmoid; desmoplastic small round cell tumor; embryonal rhabdomyosarcoma; epithelioid fibrosarcoma; epithelioid hemangioendothelioma; epithelioid sarcoma; esthesioneuroblastoma; Ewing sarcoma; extrarenal rhabdoid tumor; extraskeletal myxoid chondrosarcoma; extraskeletal osteosarcoma; fibrosarcoma; giant cell tumor; hemangiopericytoma; infantile fibrosarcoma; inflammatory myofibroblastic tumor; Kaposi sarcoma; leiomyosarcoma of bone; liposarcoma; liposarcoma of bone; malignant fibrous histiocytoma (MFH); malignant fibrous histiocytoma (MFH) of bone; malignant mesenchymoma; malignant peripheral nerve sheath tumor; mesenchymal chondrosarcoma; myxofibrosarcoma; myxoid liposarcoma; myxoinflammatory fibroblastic sarcoma; neoplasms with perivascular epitheioid cell differentiation; osteosarcoma; parosteal osteosarcoma; neoplasm with perivascular epitheioid cell differentiation; periosteal osteosarcoma; pleomorphic liposarcoma; pleomorphic rhabdomyosarcoma; PNET/extraskeletal Ewing tumor; rhabdomyosarcoma; round cell liposarcoma; small cell osteosarcoma; solitary fibrous tumor; synovial sarcoma; and telangiectatic osteosarcoma.

A carcinoma is a type of cancer that is developed from epithelial cells. Exemplary carcinoma includes, but is not limited to: an adenocarcinoma, squamous cell carcinoma, adenosquamous carcinoma, anaplastic carcinoma, large cell carcinoma, small cell carcinoma, anal cancer; appendix cancer; bile duct cancer (i.e., cholangiocarcinoma); bladder cancer; brain tumor; breast cancer; cervical cancer; colon cancer; cancer of Unknown Primary (CUP); esophageal cancer; eye cancer; fallopian tube cancer; gastroenterological cancer; kidney cancer; liver cancer; lung cancer; medulloblastoma; melanoma; oral cancer; ovarian cancer; pancreatic cancer; parathyroid disease; penile cancer; pituitary tumor; prostate cancer; rectal cancer; skin cancer; stomach cancer; testicular cancer; throat cancer; thyroid cancer; uterine cancer; vaginal cancer; and vulvar cancer. In some embodiments, the carcinoma is breast cancer. In some embodiments, the breast cancer is invasive ductal carcinoma, ductal carcinoma in situ, invasive lobular carcinoma, or lobular carcinoma in situ. In some embodiments, the carcinoma is pancreatic cancer. In some embodiments, the pancreatic cancer is adenocarcinoma, or islet cell carcinoma. In some embodiments, the carcinoma is colorectal (colon) cancer. In some embodiments, the colorectal cancer is adenocarcinoma. In some embodiments, the solid tumor is a colon polyp. In some embodiments, the colon polyp is associated with familial adenomatous polyposis. In some embodiments, the carcinoma is bladder cancer. In some embodiments, the bladder cancer is transitional cell bladder cancer, squamous cell bladder cancer, or adenocarcinoma. In some embodiments, the carcinoma is lung cancer. In some embodiments, the lung cancer is a non-small cell lung cancer. In some embodiments, the non-small cell lung cancer is adenocarcinoma, squamous-cell lung carcinoma, or large-cell lung carcinoma. In some embodiments, the lung cancer is a small cell lung cancer. In some embodiments, the carcinoma is prostate cancer. In some embodiments, the prostate cancer is adenocarcinoma or small cell carcinoma. In some embodiments, the carcinoma is ovarian cancer. In some embodiments, the ovarian cancer is epithelial ovarian cancer. In some embodiments, the carcinoma is bile duct cancer. In some embodiments, the bile duct cancer is proximal bile duct carcinoma or distal bile duct carcinoma.

As described herein, a hematologic cancer is a leukemia, a lymphoma, a myeloma, a non-Hodgkin's lymphoma, a Hodgkin's lymphoma, a T-cell malignancy, or a B-cell malignancy. In some embodiments, the hematologic cancer is a B-cell malignancy. Exemplary B-cell malignancies include, but are not limited to: chronic lymphocytic leukemia (CLL), small lymphocytic lymphoma (SLL), high risk CLL, or a non-CLL/SLL lymphoma. In some embodiments, the cancer is follicular lymphoma (FL), diffuse large B-cell lymphoma (DLBCL), mantle cell lymphoma (MCL), Waldenstrom's macroglobulinemia, multiple myeloma, extranodal marginal zone B cell lymphoma, nodal marginal zone B cell lymphoma, Burkitt's lymphoma, non-Burkitt high grade B cell lymphoma, primary mediastinal B-cell lymphoma (PMBL), immunoblastic large cell lymphoma, precursor B-lymphoblastic lymphoma, B cell prolymphocytic leukemia, lymphoplasmacytic lymphoma, splenic marginal zone lymphoma, plasma cell myeloma, plasmacytoma, mediastinal (thymic) large B cell lymphoma, intravascular large B cell lymphoma, primary effusion lymphoma, or lymphomatoid granulomatosis. In some embodiments, DLBCL is further divided into subtypes: activated B-cell diffuse large B-cell lymphoma (ABC-DLBCL) and germinal center diffuse large B-cell lymphoma (GCB DLBCL). In some embodiments, ABC-DLBCL is characterized by a CD79B mutation. In some embodiments, ABC-DLBCL is characterized by a CD79A mutation. In some embodiments, the ABC-DLBCL is characterized by a mutation in MyD88, A20, or a combination thereof. In some embodiments, the cancer is acute or chronic myelogenous (or myeloid) leukemia, myelodysplastic syndrome, and acute lymphoblastic leukemia.

In some embodiments, the ACK is Btk or a Btk homolog. In yet further embodiments, the ACK is tyrosine kinases that share homology with Btk by having a cysteine residue (including a Cys 481 residue) that forms a covalent bond with the irreversible inhibitor. In some embodiments, the ACK is HER4.

The methods described herein (which includes uses of a pharmaceutical composition to treat a disorder, or uses of a compound to form a medicament for treating a disorder) include administering to an individual in need thereof a composition containing a therapeutically effective amount of one or more irreversible Btk inhibitor compounds described herein. In some embodiments, the individual has been diagnosed with or is predisposed to develop a CNS lymphoma.

In some embodiments, are methods for treating a disorder characterized by the presence of a CNS malignancy comprising administering to an individual in need a pharmaceutical formulation of any irreversible inhibitor of Btk (or a Btk homolog) of Formula (A1-A6), Formula (B1-B6), Formula (C1-C6), Formula (D1-D6), Formula (I), or Formula (VII).

Further, in some embodiments, the irreversible Btk inhibitor compounds described herein are used to inhibit a small subset of other tyrosine kinases that share homology with Btk by having a cysteine residue (including a Cys 481 residue) that is able to form a covalent bond with the irreversible inhibitor. See, e.g., protein kinases in FIG. 7. Thus, a subset of tyrosine kinases other than Btk are also expected to be useful as therapeutic targets in a number of health conditions, including lymphomas, carcinomas, and/or sarcomas.

Symptoms, diagnostic tests, and prognostic tests for each of the above-mentioned conditions include, e.g., Harrison's Principles of Internal Medicine®,” 16th ed., 2004, The McGraw-Hill Companies, Inc. Dey et al. (2006), Cytojournal 3(24), and the “Revised European American Lymphoma” (REAL) classification system (see, e.g., the website maintained by the National Cancer Institute).

Therapeutic Uses of a Btk Inhibitor Compound and Method for Detecting and Measuring the Level of Said Btk Inhibitor in Human CNS Fluid

Described herein, in certain embodiments, are methods for treating a CNS malignancy in an individual in need thereof, comprising:

-   -   a. administering to the individual a treatment comprising a         therapeutically effective amount of a Btk inhibitor; and     -   b. monitoring the progress of the treatment by measuring the         level of the Btk inhibitor present in CNS fluid.

In some embodiments the level of the Btk inhibitor is measured from a CSF sample, thereby determining the amount of the Btk inhibitor present in the CNS fluid.

In some embodiments the method further comprises measuring the level of the Btk inhibitor in the plasma, thereby additionally monitoring the progress of the treatment through the level of the Btk inhibitor remaining in the plasma.

In some embodiments the Btk inhibitor is ibrutinib (PCI-32765).

In some embodiments the Btk inhibitor is PCI-45227.

In some embodiments the measuring of the level of the Btk inhibitor from the CSF sample is performed using liquid chromatography-tandem mass spectroscopy. In some embodiments the measuring of the level of the Btk inhibitor from the CSF sample is performed using gas chromatography-tandem mass spectroscopy.

In some embodiments the method further comprises centrifuging the CSF sample to obtain a supernatant portion and adding an internal standard to the supernatant portion of the CSF sample prior to analysis.

In some embodiments the method further comprises:

-   -   a. integrating the area-under-the curve for a peak of the Btk         inhibitor from a plot of signal intensity as a function of         elution time from the liquid chromatography-tandem mass         spectroscopy;     -   b. integrating the area-under-the curve for a peak of the         internal standard from the plot of signal intensity as a         function of elution time from the liquid chromatography-tandem         mass spectroscopy;     -   c. determining a ratio by dividing the resultant integration         from step b by the resultant integration from step a;     -   d. providing a standard calibration curve; and     -   e. calculating the concentration of the Btk inhibitor in the CSF         sample by using a power fit regression formula without         weighting.

In some embodiments the slope and intercept are calculated from the standard calibration curve.

In some embodiments the internal standard for ibrutinib is d5-PCI-32765.

In some embodiments the internal standard for PCI-45227 is d5-PCI-45227.

In some embodiments the detection range of the Btk inhibitor in the CSF sample is from about 0.01 ng/mL to about 50 ng/mL.

In some embodiments the detection range of the Btk inhibitor in the CSF sample is from about 0.1 ng/mL to about 20 ng/mL. In some embodiments the detection range of the Btk inhibitor in the CSF sample is from about 0.3 ng/mL to about 10 ng/mL. In some embodiments the detection range of the Btk inhibitor in the plasma sample is from about 1 ng/mL to about 1000 ng/mL.

In some embodiments the liquid chromatography is a high-performance liquid chromatography (HPLC).

In some embodiments the CSF sample is a stored CSF sample or a fresh CSF sample.

In some embodiments the stored CSF sample is a CSF sample stored on ice for at least 1 hour. In some embodiments the stored CSF sample is a CSF sample stored on ice for at least 2 hours. In some embodiments the stored CSF sample is a CSF sample stored on ice for at least 3 hours. In some embodiments the stored CSF sample is a CSF sample stored on ice for at least 4 hours.

In some embodiments the stored CSF sample is a CSF sample stored at −70±5° C. for at least 6 days. In some embodiments the stored CSF sample is a CSF sample stored at −70±5° C. for at least 7 days. In some embodiments the stored CSF sample is a CSF sample stored at −70±5° C. for at least 8 days. In some embodiments the stored CSF sample is a CSF sample stored at −70±5° C. for at least 9 days.

In some embodiments the stored CSF sample is a CSF sample stored at −80±5° C. for at least 6 days. In some embodiments the stored CSF sample is a CSF sample stored at −80±5° C. for at least 7 days. In some embodiments the stored CSF sample is a CSF sample stored at −80±5° C. for at least 8 days. In some embodiments the stored CSF sample is a CSF sample stored at −80±5° C. for at least 9 days.

In some embodiments the CNS malignancy is a primary CNS lymphoma.

In some embodiments the primary CNS lymphoma is a glioma.

In some embodiments the glioma is astrocytomas, ependymomas, oligodendrogliomas.

In some embodiments the CNS malignancy is astrocytic tumors such as juvenile pilocytic, subependymal, well differentiated or moderately differentiated anaplastic astrocytoma; anaplastic astrocytoma; glioblastoma multiforme; ependymal tumors such as myxopapillary and well-differentiated ependymoma, anaplastic ependymoma, ependymoblastoma; oligodendroglial tumors including well-differentiated oligodendroglioma and anaplastic oligodendroglioma; mixed tumors such as mixed astrocytoma-ependymoma, mixed astrocytoma-oligodendroglioma, mixed astrocytomaependymoma-oligodendroglioma; medulloblastoma.

In some embodiments the CNS malignancy is glioblastoma multiforme.

In some embodiments the CNS malignancy is a secondary CNS lymphoma.

In some embodiments the level of the Btk inhibitor is measured before, during, or after administering to the individual the treatment comprising a therapeutically effective amount of the Btk inhibitor.

In some embodiments the level of the Btk inhibitor is measured one, two, three, or more times during the course of the treatment.

In some embodiments the Btk inhibitor is administered once a day, two times per day, three times per day, four times per day, or five times per day.

In some embodiments the Btk inhibitor is administered at a dosage of about 40 mg/day to about 1000 mg/day. In some embodiments, the amount of the Btk inhibitor is about 80 mg/day. In some embodiments, the amount of the Btk inhibitor is about 100 mg/day. In some embodiments, the amount of the Btk inhibitor is about 140 mg/day. In some embodiments, the amount of the Btk inhibitor is about 280 mg/day. In some embodiments, the amount of the Btk inhibitor is about 420 mg/day. In some embodiments, the amount of the Btk inhibitor is about 560 mg/day. In some embodiments, the amount of the Btk inhibitor is about 700 mg/day. In some embodiments, the amount of the Btk inhibitor is about 840 mg/day. In some embodiments, the amount of the Btk inhibitor is about 980 mg/day.

In some embodiments the Btk inhibitor is administered orally.

In some embodiments the method further comprises administering a second anti-cancer agent.

Also described herein, in certain embodiments, are methods for treating a CNS malignancy in an individual in need thereof, comprising administering to the individual a treatment comprising a therapeutically effective amount of a Btk inhibitor; and monitoring the progress of the treatment by measuring the level of the Btk inhibitor present in CNS fluid as a percentage of the ratio of the concentration of the Btk inhibitor in the CSF over the concentration in the plasma. In some embodiments, the ratio of CSF concentration over the plasma concentration is expressed as a percentage for ibrutinib and PCI-45227. In some embodiments, the % CSF/plasma for ibrutinib is at least 0.5, 1.0, 1.1, 1.2, 1.3, 1.4, 1.5, 1.6, 1.7, 1.8, 1.9, 2.0, 2.1, 2.2, 2.3, 2.4, 2.5, 2.6, 2.7, 2.8, 2.9, 3.0, 3.1, 3.2, 3.3, 3.4, 3.5, 3.6, 3.7, 3.8, 3.9, 4.0, 4.1, 4.2, 4.3, 4.4, 4.5, 4.6, 4.7, 4.8, 4.9, 5.0, 5.5, 6.0, 6.5, 7.0, 7.5, 8.0, 8.5, 9.0, 9.5, 10.0, 10.5, 11.0, 11.5, 12.0, 12.5, 13.0, 14, 15, or more. In some embodiments, the % CSF/plasma for ibrutinib is no more than 0.5, 1.0, 1.1, 1.2, 1.3, 1.4, 1.5, 1.6, 1.7, 1.8, 1.9, 2.0, 2.1, 2.2, 2.3, 2.4, 2.5, 2.6, 2.7, 2.8, 2.9, 3.0, 3.1, 3.2, 3.3, 3.4, 3.5, 3.6, 3.7, 3.8, 3.9, 4.0, 4.1, 4.2, 4.3, 4.4, 4.5, 4.6, 4.7, 4.8, 4.9, 5.0, 5.5, 6.0, 6.5, 7.0, 7.5, 8.0, 8.5, 9.0, 9.5, 10.0, 10.5, 11.0, 11.5, 12.0, 12.5, 13.0, 14, 15, or less. In some embodiments, the % CSF/plasma for ibrutinib is about 2.5 to about 4.0, or about 3.0 to about 3.5. In some embodiments, the % CSF/plasma for PCI-45227 is at least 0.5, 1.0, 1.1, 1.2, 1.3, 1.4, 1.5, 1.6, 1.7, 1.8, 1.9, 2.0, 2.1, 2.2, 2.3, 2.4, 2.5, 2.6, 2.7, 2.8, 2.9, 3.0, 3.1, 3.2, 3.3, 3.4, 3.5, 3.6, 3.7, 3.8, 3.9, 4.0, 4.1, 4.2, 4.3, 4.4, 4.5, 4.6, 4.7, 4.8, 4.9, 5.0, 5.5, 6.0, 6.1, 6.2, 6.3, 6.4, 6.5, 6.6, 6.7, 6.8, 6.9, 7.0, 7.1, 7.2, 7.3, 7.4, 7.5, 7.6, 7.7, 7.8, 7.9, 8.0, 8.1, 8.2, 8.3, 8.4, 8.5, 8.6, 8.7, 8.8, 8.9, 9.0, 9.1, 9.2, 9.3, 9.4, 9.5, 9.6, 9.7, 9.8, 9.9, 10.0, 10.5, 11.0, 11.5, 12.0, 12.5, 13.0, 14, 15, or more. In some embodiments, the % CSF/plasma for PCI-45227 is no more than 0.5, 1.0, 1.1, 1.2, 1.3, 1.4, 1.5, 1.6, 1.7, 1.8, 1.9, 2.0, 2.1, 2.2, 2.3, 2.4, 2.5, 2.6, 2.7, 2.8, 2.9, 3.0, 3.1, 3.2, 3.3, 3.4, 3.5, 3.6, 3.7, 3.8, 3.9, 4.0, 4.1, 4.2, 4.3, 4.4, 4.5, 4.6, 4.7, 4.8, 4.9, 5.0, 5.5, 6.0, 6.1, 6.2, 6.3, 6.4, 6.5, 6.6, 6.7, 6.8, 6.9, 7.0, 7.1, 7.2, 7.3, 7.4, 7.5, 7.6, 7.7, 7.8, 7.9, 8.0, 8.1, 8.2, 8.3, 8.4, 8.5, 8.6, 8.7, 8.8, 8.9, 9.0, 9.1, 9.2, 9.3, 9.4, 9.5, 9.6, 9.7, 9.8, 9.9, 10.0, 10.5, 11.0, 11.5, 12.0, 12.5, 13.0, 14, 15, or less. In some embodiments, the % CSF/plasma for PCI-45227 is about 6.0 to about 9.0, or bout 6.2 to about 8.5. In some embodiments, the concentrations of CSF and plasma for ibrutinib and PCI-45227 were measured on days 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 28, 1 month, 2 months, 3 months, or more. In some embodiments, the concentrations of CSF and plasma for ibrutinib and PCI-45227 were measured on days 0, day 1, and 1 month. In some embodiments, the concentrations of CSF and plasma for ibrutinib and PCI-45227 were measured at about 0 h, 1 h, 2 h, 3 h, 4 h, or more post ibrutinib administration. In some embodiments, the concentrations of CSF and plasma for ibrutinib and PCI-45227 were measured at about 0 h, 2 h, or 3 h post ibrutinib administration.

A number of animal models are useful for establishing a range of therapeutically effective doses of irreversible inhibitors, including irreversible Btk inhibitor compounds for treating any of the foregoing diseases.

In one embodiment, the therapeutic efficacy of the compound for one of the foregoing diseases is optimized during a course of treatment. For example, an individual being treated optionally undergoes a diagnostic evaluation to correlate the relief of disease symptoms or pathologies to inhibition of in vivo Btk activity achieved by administering a given dose of an irreversible Btk inhibitor. Cellular assays are used to determine in vivo activity of Btk in the presence or absence of an irreversible Btk inhibitor. For example, since activated Btk is phosphorylated at tyrosine 223 (Y223) and tyrosine 551 (Y551), phospho-specific immunocytochemical staining of P-Y223 or P-Y551-positive cells are used to detect or quantify activation of Bkt in a population of cells (e.g., by FACS analysis of stained vs unstained cells). See, e.g., Nisitani et al. (1999), Proc. Natl. Acad. Sci, USA 96:2221-2226. Thus, the amount of the Btk inhibitor compound that is administered to an individual is optionally increased or decreased as needed so as to maintain a level of Btk inhibition optimal for treating the subject's disease state.

Combination Treatments

In some embodiments, the irreversible Btk inhibitor compositions described herein are used in combination with other well known therapeutic reagents that are selected for their therapeutic value for the condition to be treated. In general, the compositions described herein and, in embodiments where combinational therapy is employed, other agents do not have to be administered in the same pharmaceutical composition, and are optionally, because of different physical and chemical characteristics, have to be administered by different routes. The initial administration is made, for example, according to established protocols, and then, based upon the observed effects, the dosage, modes of administration and times of administration are modified.

In certain instances, it is appropriate to administer at least one irreversible Btk inhibitor compound described herein in combination with another therapeutic agent. By way of example only, if one of the side effects experienced by an individual upon receiving one of the irreversible Btk inhibitor compounds described herein is nausea, then it is appropriate to administer an anti-nausea agent in combination with the initial therapeutic agent. Or, by way of example only, the therapeutic effectiveness of one of the compounds described herein is enhanced by administration of an adjuvant (i.e., by itself the adjuvant has minimal therapeutic benefit, but in combination with another therapeutic agent, the overall therapeutic benefit to the patient is enhanced). Or, by way of example only, the benefit experienced by an individual is increased by administering one of the compounds described herein with another therapeutic agent (which also includes a therapeutic regimen) that also has therapeutic benefit. In any case, regardless of the disease, disorder being treated, the overall benefit experienced by the patient is in some embodiments simply additive of the two therapeutic agents or in other embodiments, the patient experiences a synergistic benefit.

The particular choice of compounds used will depend upon the diagnosis of the attending physicians and their judgment of the condition of the patient and the appropriate treatment protocol. The compounds are optionally administered concurrently (e.g., simultaneously, essentially simultaneously or within the same treatment protocol) or sequentially, depending upon the nature of the disorder, the condition of the patient, and the actual choice of compounds used. The determination of the order of administration, and the number of repetitions of administration of each therapeutic agent during a treatment protocol, is based on an evaluation of the disease being treated and the condition of the patient.

In some embodiments, therapeutically-effective dosages vary when the drugs are used in treatment combinations. Methods for experimentally determining therapeutically-effective dosages of drugs and other agents for use in combination treatment regimens are described in the literature. For example, the use of metronomic dosing, i.e., providing more frequent, lower doses in order to minimize toxic side effects, has been described extensively in the literature Combination treatment further includes periodic treatments that start and stop at various times to assist with the clinical management of the patient.

For combination therapies described herein, dosages of the co-administered compounds will of course vary depending on the type of co-drug employed, on the specific drug employed, on the disorder being treated and so forth. In addition, when co-administered with one or more biologically active agents, the compound provided herein is administered either simultaneously with the biologically active agent(s), or sequentially. If administered sequentially, the attending physician will decide on the appropriate sequence of administering protein in combination with the biologically active agent(s).

In any case, the multiple therapeutic agents (one of which is a compound of Formula (A1-A6), (B1-B6), (C1-C6), or (D1-D6) described herein) are optionally administered in any order or even simultaneously. If simultaneously, the multiple therapeutic agents are optionally provided in a single, unified form, or in multiple forms (by way of example only, either as a single pill or as two separate pills). In some embodiments, one of the therapeutic agents is given in multiple doses, or both are given as multiple doses. If not simultaneous, the timing between the multiple doses is from about more than zero weeks to less than about four weeks. In addition, the combination methods, compositions and formulations are not to be limited to the use of only two agents; the use of multiple therapeutic combinations are also envisioned.

It is understood that the dosage regimen to treat, prevent, or ameliorate the condition(s) for which relief is sought, can be modified in accordance with a variety of factors. These factors include the disorder from which the subject suffers, as well as the age, weight, sex, diet, and medical condition of the subject. Thus, the dosage regimen actually employed can vary widely and therefore can deviate from the dosage regimens set forth herein.

In some embodiments, the pharmaceutical agents which make up the combination therapy disclosed herein are administered in a combined dosage form, or in separate dosage forms intended for substantially simultaneous administration. In some embodiments, the pharmaceutical agents that make up the combination therapy are administered sequentially, with either therapeutic compound being administered by a regimen calling for two-step administration. In some embodiments, the two-step administration regimen calls for sequential administration of the active agents or spaced-apart administration of the separate active agents. The time period between the multiple administration steps ranges from a few minutes to several hours, depending upon the properties of each pharmaceutical agent, such as potency, solubility, bioavailability, plasma half-life and kinetic profile of the pharmaceutical agent. In some embodiments, circadian variation of the target molecule concentration determines the optimal dose interval.

In addition, the compounds described herein also are optionally used in combination with procedures that provide additional or synergistic benefit to the patient. By way of example only, patients are expected to find therapeutic and/or prophylactic benefit in the methods described herein, wherein pharmaceutical composition of a compound disclosed herein and/or combinations with other therapeutics are combined with genetic testing to determine whether that individual is a carrier of a mutant gene that is known to be correlated with certain diseases or conditions.

The compounds described herein and combination therapies are administered before, during or after the occurrence of a disorder, and the timing of administering the composition containing a compound is variable. In some embodiments, the compounds are used as a prophylactic and are administered continuously to subjects with a propensity to develop conditions or diseases in order to prevent the occurrence of the disorder. In some embodiments, the compounds and compositions are administered to an individual during or as soon as possible after the onset of the symptoms. In some embodiments, the administration of the compounds is initiated within the first 48 hours of the onset of the symptoms, within the first 6 hours of the onset of the symptoms, or within 3 hours of the onset of the symptoms. In some embodiments, the initial administration is via any route practical, such as, for example, an intravenous injection, a bolus injection, infusion over 5 minutes to about 5 hours, a pill, a capsule, transdermal patch, buccal delivery, and the like, or combination thereof. A compound should be administered as soon as is practicable after the onset of a disorder is detected or suspected, and for a length of time necessary for the treatment of the disease, such as, for example, from about 1 month to about 3 months. The length of treatment can vary for each subject, and the length can be determined using the known criteria. In some embodiments, the compound or a formulation containing the compound is administered for at least 2 weeks, between about 1 month to about 5 years, or from about 1 month to about 3 years.

Exemplary Therapeutic Agents for Use in Combination with an Irreversible Inhibitor Compound

In some embodiments, where the subject is suffering from or at risk of suffering from a disorder characterized by the presence or development of one or more CNS malignancies, the subject is treated with an irreversible Btk inhibitor compound in any combination with one or more other anti-cancer agents. In some embodiments, one or more of the following: afinitor (everolimus), afinitor disperz, avastin (bevacizumab), becenum (carmustine), BiCNU, Gliadel, Gliadel wafer, lomustine, procarbazine, methazolastone (temozolomide), vincristine, and temodor.

In another embodiment, the is a method for treating a CNS malignancy comprising treating a subject with an irreversible Btk inhibitor compound in compound with one or more of the following: irinotecan, cisplatin, carboplatin, methotrexate, etoposide, bleomycin, vinblastine, actinomycin (dactinomycin), cyclophosphamide, and ifosfamide.

Examples of anti-cancer agents include, but are not limited to, any of the following: gossyphol, genasense, polyphenol E, Chlorofusin, all trans-retinoic acid (ATRA), bryostatin, tumor necrosis factor-related apoptosis-inducing ligand (TRAIL), 5-aza-2′-deoxycytidine, all trans retinoic acid, doxorubicin, vincristine, etoposide, gemcitabine, imatinib (Gleevec®), geldanamycin, 17-N-Allylamino-17-Demethoxygeldanamycin (17-AAG), flavopiridol, LY294002, bortezomib, trastuzumab, BAY 11-7082, PKC412, or PD184352, Taxol™, also referred to as “paclitaxel”, which is a well-known anti-cancer drug which acts by enhancing and stabilizing microtubule formation, and analogs of Taxol™, such as Taxotere™. Compounds that have the basic taxane skeleton as a common structure feature, have also been shown to have the ability to arrest cells in the G2-M phases due to stabilized microtubules and, in some embodiments, are useful for treating cancer in combination with the compounds described herein.

Further examples of anti-cancer agents for use in combination with an irreversible Btk inhibitor compound include inhibitors of mitogen-activated protein kinase signaling, e.g., U0126, PD98059, PD184352, PD0325901, ARRY-142886, SB239063, SP600125, BAY 43-9006, wortmannin, or LY294002; Syk inhibitors; mTOR inhibitors; and antibodies (e.g., rituxan).

Other anti-cancer agents for use in combination with an irreversible Btk inhibitor compound include Adriamycin, Dactinomycin, Bleomycin, Vinblastine, Cisplatin, acivicin; aclarubicin; acodazole hydrochloride; acronine; adozelesin; aldesleukin; altretamine; ambomycin; ametantrone acetate; aminoglutethimide; amsacrine; anastrozole; anthramycin; asparaginase; asperlin; azacitidine; azetepa; azotomycin; batimastat; benzodepa; bicalutamide; bisantrene hydrochloride; bisnafide dimesylate; bizelesin; bleomycin sulfate; brequinar sodium; bropirimine; busulfan; cactinomycin; calusterone; caracemide; carbetimer; carboplatin; carmustine; carubicin hydrochloride; carzelesin; cedefingol; chlorambucil; cirolemycin; cladribine; crisnatol mesylate; cyclophosphamide; cytarabine; dacarbazine; daunorubicin hydrochloride; decitabine; dexormaplatin; dezaguanine; dezaguanine mesylate; diaziquone; doxorubicin; doxorubicin hydrochloride; droloxifene; droloxifene citrate; dromostanolone propionate; duazomycin; edatrexate; eflornithine hydrochloride; elsamitrucin; enloplatin; enpromate; epipropidine; epirubicin hydrochloride; erbulozole; esorubicin hydrochloride; estramustine; estramustine phosphate sodium; etanidazole; etoposide; etoposide phosphate; etoprine; fadrozole hydrochloride; fazarabine; fenretinide; floxuridine; fludarabine phosphate; fluorouracil; flurocitabine; fosquidone; fostriecin sodium; gemcitabine; gemcitabine hydrochloride; hydroxyurea; idarubicin hydrochloride; ifosfamide; iimofosine; interleukin I1 (including recombinant interleukin II, or rlL2), interferon alfa-2a; interferon alfa-2b; interferon alfa-n1; interferon alfa-n3; interferon beta-1 a; interferon gamma-1 b; iproplatin; irinotecan hydrochloride; lanreotide acetate; letrozole; leuprolide acetate; liarozole hydrochloride; lometrexol sodium; lomustine; losoxantrone hydrochloride; masoprocol; maytansine; mechlorethamine hydrochloride; megestrol acetate; melengestrol acetate; melphalan; menogaril; mercaptopurine; methotrexate; methotrexate sodium; metoprine; meturedepa; mitindomide; mitocarcin; mitocromin; mitogillin; mitomalcin; mitomycin; mitosper; mitotane; mitoxantrone hydrochloride; mycophenolic acid; nocodazoie; nogalamycin; ormaplatin; oxisuran; pegaspargase; peliomycin; pentamustine; peplomycin sulfate; perfosfamide; pipobroman; piposulfan; piroxantrone hydrochloride; plicamycin; plomestane; porfimer sodium; porfiromycin; prednimustine; procarbazine hydrochloride; puromycin; puromycin hydrochloride; pyrazofurin; riboprine; rogletimide; safingol; safingol hydrochloride; semustine; simtrazene; sparfosate sodium; sparsomycin; spirogermanium hydrochloride; spiromustine; spiroplatin; streptonigrin; streptozocin; sulofenur; talisomycin; tecogalan sodium; tegafur; teloxantrone hydrochloride; temoporfin; teniposide; teroxirone; testolactone; thiamiprine; thioguanine; thiotepa; tiazofurin; tirapazamine; toremifene citrate; trestolone acetate; triciribine phosphate; trimetrexate; trimetrexate glucuronate; triptorelin; tubulozole hydrochloride; uracil mustard; uredepa; vapreotide; verteporfin; vinblastine sulfate; vincristine sulfate; vindesine; vindesine sulfate; vinepidine sulfate; vinglycinate sulfate; vinleurosine sulfate; vinorelbine tartrate; vinrosidine sulfate; vinzolidine sulfate; vorozole; zeniplatin; zinostatin; zorubicin hydrochloride.

Other anti-cancer agents for use in combination with an irreversible Btk inhibitor compound include: 20-epi-1, 25 dihydroxyvitamin D3; 5-ethynyluracil; abiraterone; aclarubicin; acylfulvene; adecypenol; adozelesin; aldesleukin; ALL-TK antagonists; altretamine; ambamustine; amidox; amifostine; aminolevulinic acid; amrubicin; amsacrine; anagrelide; anastrozole; andrographolide; angiogenesis inhibitors; antagonist D; antagonist G; antarelix; anti-dorsalizing morphogenetic protein-1; antiandrogen, prostatic carcinoma; antiestrogen; antineoplaston; antisense oligonucleotides; aphidicolin glycinate; apoptosis gene modulators; apoptosis regulators; apurinic acid; ara-CDP-DL-PTBA; arginine deaminase; asulacrine; atamestane; atrimustine; axinastatin 1; axinastatin 2; axinastatin 3; azasetron; azatoxin; azatyrosine; baccatin III derivatives; balanol; batimastat; BCR/ABL antagonists; benzochlorins; benzoylstaurosporine; beta lactam derivatives; beta-alethine; betaclamycin B; betulinic acid; bFGF inhibitor; bicalutamide; bisantrene; bisaziridinylspermine; bisnafide; bistratene A; bizelesin; breflate; bropirimine; budotitane; buthionine sulfoximine; calcipotriol; calphostin C; camptothecin derivatives; canarypox IL-2; capecitabine; carboxamide-amino-triazole; carboxyamidotriazole; CaRest M3; CARN 700; cartilage derived inhibitor; carzelesin; casein kinase inhibitors (ICOS); castanospermine; cecropin B; cetrorelix; chlorins; chloroquinoxaline sulfonamide; cicaprost; cis-porphyrin; cladribine; clomifene analogues; clotrimazole; collismycin A; collismycin B; combretastatin A4; combretastatin analogue; conagenin; crambescidin 816; crisnatol; cryptophycin 8; cryptophycin A derivatives; curacin A; cyclopentanthraquinones; cycloplatam; cypemycin; cytarabine ocfosfate; cytolytic factor; cytostatin; dacliximab; decitabine; dehydrodidemnin B; deslorelin; dexamethasone; dexifosfamide; dexrazoxane; dexverapamil; diaziquone; didemnin B; didox; diethylnorspermine; dihydro-5-azacytidine; 9-dioxamycin; diphenyl spiromustine; docosanol; dolasetron; doxifluridine; droloxifene; dronabinol; duocarmycin SA; ebselen; ecomustine; edelfosine; edrecolomab; eflornithine; elemene; emitefur; epirubicin; epristeride; estramustine analogue; estrogen agonists; estrogen antagonists; etanidazole; etoposide phosphate; exemestane; fadrozole; fazarabine; fenretinide; filgrastim; finasteride; flavopiridol; flezelastine; fluasterone; fludarabine; fluorodaunorunicin hydrochloride; forfenimex; formestane; fostriecin; fotemustine; gadolinium texaphyrin; gallium nitrate; galocitabine; ganirelix; gelatinase inhibitors; gemcitabine; glutathione inhibitors; hepsulfam; heregulin; hexamethylene bisacetamide; hypericin; ibandronic acid; idarubicin; idoxifene; idramantone; ilmofosine; ilomastat; imidazoacridones; imiquimod; immunostimulant peptides; insulin-like growth factor-1 receptor inhibitor; interferon agonists; interferons; interleukins; iobenguane; iododoxorubicin; ipomeanol, 4-; iroplact; irsogladine; isobengazole; isohomohalicondrin B; itasetron; jasplakinolide; kahalalide F; lamellarin-N triacetate; lanreotide; leinamycin; lenograstim; lentinan sulfate; leptolstatin; letrozole; leukemia inhibiting factor; leukocyte alpha interferon; leuprolide+estrogen+progesterone; leuprorelin; levamisole; liarozole; linear polyamine analogue; lipophilic disaccharide peptide; lipophilic platinum compounds; lissoclinamide 7; lobaplatin; lombricine; lometrexol; lonidamine; losoxantrone; lovastatin; loxoribine; lurtotecan; lutetium texaphyrin; lysofylline; lytic peptides; maitansine; mannostatin A; marimastat; masoprocol; maspin; matrilysin inhibitors; matrix metalloproteinase inhibitors; menogaril; merbarone; meterelin; methioninase; metoclopramide; MIF inhibitor; mifepristone; miltefosine; mirimostim; mismatched double stranded RNA; mitoguazone; mitolactol; mitomycin analogues; mitonafide; mitotoxin fibroblast growth factor-saporin; mitoxantrone; mofarotene; molgramostim; monoclonal antibody, human chorionic gonadotrophin; monophosphoryl lipid A+myobacterium cell wall sk; mopidamol; multiple drug resistance gene inhibitor; multiple tumor suppressor 1-based therapy; mustard anticancer agent; mycaperoxide B; mycobacterial cell wall extract; myriaporone; N-acetyldinaline; N-substituted benzamides; nafarelin; nagrestip; naloxone+pentazocine; napavin; naphterpin; nartograstim; nedaplatin; nemorubicin; neridronic acid; neutral endopeptidase; nilutamide; nisamycin; nitric oxide modulators; nitroxide antioxidant; nitrullyn; O6-benzylguanine; octreotide; okicenone; oligonucleotides; onapristone; ondansetron; ondansetron; oracin; oral cytokine inducer; ormaplatin; osaterone; oxaliplatin; oxaunomycin; palauamine; palmitoylrhizoxin; pamidronic acid; panaxytriol; panomifene; parabactin; pazelliptine; pegaspargase; peldesine; pentosan polysulfate sodium; pentostatin; pentrozole; perflubron; perfosfamide; perillyl alcohol; phenazinomycin; phenylacetate; phosphatase inhibitors; picibanil; pilocarpine hydrochloride; pirarubicin; piritrexim; placetin A; placetin B; plasminogen activator inhibitor; platinum complex; platinum compounds; platinum-triamine complex; porfimer sodium; porfiromycin; prednisone; propyl bis-acridone; prostaglandin J2; proteasome inhibitors; protein A-based immune modulator; protein kinase C inhibitor; protein kinase C inhibitors, microalgal; protein tyrosine phosphatase inhibitors; purine nucleoside phosphorylase inhibitors; purpurins; pyrazoloacridine; pyridoxylated hemoglobin polyoxyethylerie conjugate; raf antagonists; raltitrexed; ramosetron; ras farnesyl protein transferase inhibitors; ras inhibitors; ras-GAP inhibitor; retelliptine demethylated; rhenium Re 186 etidronate; rhizoxin; ribozymes; RII retinamide; rogletimide; rohitukine; romurtide; roquinimex; rubiginone B1; ruboxyl; safingol; saintopin; SarCNU; sarcophytol A; sargramostim; Sdi 1 mimetics; semustine; senescence derived inhibitor 1; sense oligonucleotides; signal transduction inhibitors; signal transduction modulators; single chain antigen-binding protein; sizofiran; sobuzoxane; sodium borocaptate; sodium phenylacetate; solverol; somatomedin binding protein; sonermin; sparfosic acid; spicamycin D; spiromustine; splenopentin; spongistatin 1; squalamine; stem cell inhibitor; stem-cell division inhibitors; stipiamide; stromelysin inhibitors; sulfinosine; superactive vasoactive intestinal peptide antagonist; suradista; suramin; swainsonine; synthetic glycosaminoglycans; tallimustine; tamoxifen methiodide; tauromustine; tazarotene; tecogalan sodium; tegafur; tellurapyrylium; telomerase inhibitors; temoporfin; temozolomide; teniposide; tetrachlorodecaoxide; tetrazomine; thaliblastine; thiocoraline; thrombopoietin; thrombopoietin mimetic; thymalfasin; thymopoietin receptor agonist; thymotrinan; thyroid stimulating hormone; tin ethyl etiopurpurin; tirapazamine; titanocene bichloride; topsentin; toremifene; totipotent stem cell factor; translation inhibitors; tretinoin; triacetyluridine; triciribine; trimetrexate; triptorelin; tropisetron; turosteride; tyrosine kinase inhibitors; tyrphostins; UBC inhibitors; ubenimex; urogenital sinus-derived growth inhibitory factor; urokinase receptor antagonists; vapreotide; variolin B; vector system, erythrocyte gene therapy; velaresol; veramine; verdins; verteporfin; vinorelbine; vinxaltine; vitaxin; vorozole; zanoterone; zeniplatin; zilascorb; and zinostatin stimalamer.

Yet other anticancer agents for use in combination with an irreversible Btk inhibitor compound include alkylating agents, antimetabolites, natural products, or hormones, e.g., nitrogen mustards (e.g., mechloroethamine, cyclophosphamide, chlorambucil, etc.), alkyl sulfonates (e.g., busulfan), nitrosoureas (e.g., carmustine, lomusitne, ete.), or triazenes (decarbazine, etc.). Examples of antimetabolites include but are not limited to folic acid analog (e.g., methotrexate), or pyrimidine analogs (e.g., Cytarabine), purine analogs (e.g., mercaptopurine, thioguanine, pentostatin).

Examples of natural products useful in combination with an irreversible Btk inhibitor compound include but are not limited to vinca alkaloids (e.g., vinblastin, vincristine), epipodophyllotoxins (e.g., etoposide), antibiotics (e.g., daunorubicin, doxorubicin, bleomycin), enzymes (e.g., L-asparaginase), or biological response modifiers (e.g., interferon alpha).

Examples of alkylating agents for use employed in combination an irreversible Btk inhibitor compound include, but are not limited to, nitrogen mustards (e.g., mechloroethamine, cyclophosphamide, chlorambucil, meiphalan, etc.), ethylenimine and methylmelamines (e.g., hexamethlymelamine, thiotepa), alkyl sulfonates (e.g., busulfan), nitrosoureas (e.g., carmustine, lomusitne, semustine, streptozocin, etc.), or triazenes (decarbazine, ete.). Examples of antimetabolites include, but are not limited to folic acid analog (e.g., methotrexate), or pyrimidine analogs (e.g., fluorouracil, floxouridine, Cytarabine), purine analogs (e.g., mercaptopurine, thioguanine, pentostatin.

Examples of hormones and antagonists useful in combination with an irreversible Btk inhibitor compound include, but are not limited to, adrenocorticosteroids (e.g., prednisone), progestins (e.g., hydroxyprogesterone caproate, megestrol acetate, medroxyprogesterone acetate), estrogens (e.g., diethlystilbestrol, ethinyl estradiol), antiestrogen (e.g., tamoxifen), androgens (e.g., testosterone propionate, fluoxymesterone), antiandrogen (e.g., flutamide), gonadotropin releasing hormone analog (e.g., leuprolide). Other agents for use in the methods and compositions described herein for the treatment or prevention of cancer include platinum coordination complexes (e.g., cisplatin, carboblatin), anthracenedione (e.g., mitoxantrone), substituted urea (e.g., hydroxyurea), methyl hydrazine derivative (e.g., procarbazine), adrenocortical suppressant (e.g., mitotane, aminoglutethimide).

Examples of anti-cancer agents which act by arresting cells in the G2-M phases due to stabilized microtubules and which can be used in combination with an irreversible Btk inhibitor compound include without limitation marketed drugs and drugs in development.

Where the subject is suffering from or at risk of suffering from a thromboembolic disorder (e.g., stroke), in some embodiments, the individual is treated with an irreversible Btk inhibitor compound in any combination with one or more other anti-thromboembolic agents. Examples of anti-thromboembolic agents include, but are not limited any of the following: thrombolytic agents (e.g., alteplase anistreplase, streptokinase, urokinase, or tissue plasminogen activator), heparin, tinzaparin, warfarin, dabigatran (e.g., dabigatran etexilate), factor Xa inhibitors (e.g., fondaparinux, draparinux, rivaroxaban, DX-9065a, otamixaban, LY517717, or YM150), factor VIIa inhibitors, ticlopidine, clopidogrel, CS-747 (prasugrel, LY640315), ximelagatran, or BIBR 1048.

Pharmaceutical Composition/Formulation

Pharmaceutical compositions are formulated in a conventional manner using one or more physiologically acceptable carriers including excipients and auxiliaries which facilitate processing of the active compounds into preparations which can be used pharmaceutically. Proper formulation is dependent upon the route of administration chosen. A summary of pharmaceutical compositions described herein is found, for example, in Remington: The Science and Practice of Pharmacy, Nineteenth Ed (Easton, Pa.: Mack Publishing Company, 1995); Hoover, John E., Remington's Pharmaceutical Sciences, Mack Publishing Co., Easton, Pa. 1975; Liberman, H. A. and Lachman, L., Eds., Pharmaceutical Dosage Forms, Marcel Decker, New York, N. Y., 1980; and Pharmaceutical Dosage Forms and Drug Delivery Systems, Seventh Ed. (Lippincott Williams & Wilkins 1999).

A pharmaceutical composition, as used herein, refers to a mixture of a compound described herein, such as, for example, compounds of any of Formula (A1-A6), Formula (B1-B6), Formula (C1-C6), Formula (D1-D6), Formula (I), or Formula (VII), with other chemical components, such as carriers, stabilizers, diluents, dispersing agents, suspending agents, thickening agents, and/or excipients. The pharmaceutical composition facilitates administration of the compound to an organism. In practicing the methods of treatment or use provided herein, therapeutically effective amounts of compounds described herein are administered in a pharmaceutical composition to a mammal having a disorder to be treated. Preferably, the mammal is a human. The compounds can be used singly or in combination with one or more therapeutic agents as components of mixtures.

The pharmaceutical formulations described herein are administered to an individual by any suitable administration route, including but not limited to, oral, parenteral (e.g., intravenous, subcutaneous, intramuscular), intranasal, buccal, topical, rectal, or transdermal administration routes. The pharmaceutical formulations described herein include, but are not limited to, aqueous liquid dispersions, self-emulsifying dispersions, solid solutions, liposomal dispersions, aerosols, solid dosage forms, powders, immediate release formulations, controlled release formulations, fast melt formulations, tablets, capsules, pills, delayed release formulations, extended release formulations, pulsatile release formulations, multiparticulate formulations, and mixed immediate and controlled release formulations.

Pharmaceutical compositions including a compound described herein are optionally manufactured in a conventional manner, such as, by way of example only, by means of conventional mixing, dissolving, granulating, dragee-making, levigating, emulsifying, encapsulating, entrapping or compression processes.

The pharmaceutical compositions will include at least one compound described herein, such as, for example, a compound of any of Formula (A1-A6), Formula (B1-B6), Formula (C1-C6), Formula (D1-D6), Formula (I), or Formula (VII), as an active ingredient in free-acid or free-base form, or in a pharmaceutically acceptable salt form. In addition, the methods and pharmaceutical compositions described herein include the use of N-oxides, crystalline forms (also known as polymorphs), as well as active metabolites of these compounds having the same type of activity. In some situations, compounds exist as tautomers. All tautomers are included within the scope of the compounds presented herein. Additionally, in some embodiments, the compounds described herein exist in unsolvated as well as solvated forms with pharmaceutically acceptable solvents such as water, ethanol, and the like. The solvated forms of the compounds presented herein are also considered to be disclosed herein.

A “carrier” or “carrier materials” includes excipients in pharmaceutics and is selected on the basis of compatibility with compounds disclosed herein, such as, compounds of any of Formula (A1-A6), Formula (B1-B6), Formula (C1-C6), Formula (D1-D6), Formula (I), or Formula (VII), and the release profile properties of the desired dosage form. Exemplary carrier materials include, e.g., binders, suspending agents, disintegration agents, filling agents, surfactants, solubilizers, stabilizers, lubricants, wetting agents, diluents, and the like. See, e.g., Remington: The Science and Practice of Pharmacy, Nineteenth Ed (Easton, Pa.: Mack Publishing Company, 1995); Hoover, John E., Remington's Pharmaceutical Sciences, Mack Publishing Co., Easton, Pa. 1975; Liberman, H. A. and Lachman, L., Eds., Pharmaceutical Dosage Forms, Marcel Decker, New York, N. Y., 1980; and Pharmaceutical Dosage Forms and Drug Delivery Systems, Seventh Ed. (Lippincott Williams & Wilkins 1999).

A “measurable serum concentration” or “measurable plasma concentration” describes the blood serum or blood plasma concentration, typically measured in mg, jig, or ng of therapeutic agent per ml, dl, or 1 of blood serum, absorbed into the bloodstream after administration. As used herein, measurable plasma concentrations are typically measured in ng/ml or μg/ml.

“Pharmacodynamics” refers to the factors which determine the biologic response observed relative to the concentration of drug at a site of action. “Pharmacokinetics” refers to the factors which determine the attainment and maintenance of the appropriate concentration of drug at a site of action.

“Steady state,” as used herein, is when the amount of drug administered is equal to the amount of drug eliminated within one dosing interval resulting in a plateau or constant plasma drug exposure.

Dosage Forms

Moreover, the pharmaceutical compositions described herein, which include a compound of any of Formula (A1-A6), Formula (B1-B6), Formula (C1-C6), Formula (D1-D6), Formula (I), or Formula (VII) are formulated into any suitable dosage form, including but not limited to, aqueous oral dispersions, liquids, gels, syrups, elixirs, slurries, suspensions and the like, for oral ingestion by an individual to be treated, solid oral dosage forms, aerosols, controlled release formulations, fast melt formulations, effervescent formulations, lyophilized formulations, tablets, powders, pills, dragees, capsules, delayed release formulations, extended release formulations, pulsatile release formulations, multiparticulate formulations, and mixed immediate release and controlled release formulations.

The pharmaceutical solid dosage forms described herein optionally include a compound described herein and one or more pharmaceutically acceptable additives such as a compatible carrier, binder, filling agent, suspending agent, flavoring agent, sweetening agent, disintegrating agent, dispersing agent, surfactant, lubricant, colorant, diluent, solubilizer, moistening agent, plasticizer, stabilizer, penetration enhancer, wetting agent, anti-foaming agent, antioxidant, preservative, or one or more combination thereof. In still other aspects, using standard coating procedures, such as those described in Remington's Pharmaceutical Sciences, 20th Edition (2000), a film coating is provided around the formulation of the compound of any of Formula (A1-A6), Formula (B1-B6), Formula (C1-C6), Formula (D1-D6), Formula (I), or Formula (VII). In one embodiment, some or all of the particles of the compound of any of Formula (A1-A6), Formula (B1-B6), Formula (C1-C6), Formula (D1-D6), Formula (I), or Formula (VII), are coated. In another embodiment, some or all of the particles of the compound of any of Formula (A1-A6), Formula (B1-B6), Formula (C1-C6), Formula (D1-D6), Formula (I), or Formula (VII), are microencapsulated. In still another embodiment, the particles of the compound of any of Formula (A1-A6), Formula (B1-B6), Formula (C1-C6), Formula (D1-D6), Formula (I), or Formula (VII), are not microencapsulated and are uncoated.

Examples of Methods of Dosing and Treatment Regimens

In some embodiments, the compounds described herein are used in the preparation of medicaments for the inhibition of Btk or a homolog thereof, or for the treatment of diseases or conditions that benefit, at least in part, from inhibition of Btk or a homolog thereof. In some embodiments, the compounds described herein are used in the preparation of medicaments for the inhibition of HER4 or a homolog thereof, or for the treatment of diseases or conditions that benefit, at least in part, from inhibition of HER4 or a homolog thereof. In addition, a method for treating any of the diseases or conditions described herein in an individual in need of such treatment, involves administration of pharmaceutical compositions containing at least one compound of any of Formula (A1-A6), Formula (B1-B6), Formula (C1-C6), Formula (D1-D6), Formula (I), or Formula (VII), described herein, or a pharmaceutically acceptable salt, pharmaceutically acceptable N-oxide, pharmaceutically active metabolite, pharmaceutically acceptable prodrug, or pharmaceutically acceptable solvate thereof, in therapeutically effective amounts to said subject.

In some embodiments, the compositions containing the compound(s) described herein are administered for prophylactic and/or therapeutic treatments. In therapeutic applications, the compositions are administered to an individual already suffering from a disorder, in an amount sufficient to cure or at least partially arrest the symptoms of the disorder. Amounts effective for this use will depend on the severity and course of the disorder, previous therapy, the patient's health status, weight, and response to the drugs, and the judgment of the treating physician.

In prophylactic applications, compositions containing the compounds described herein are administered to an individual susceptible to or otherwise at risk of a particular disease, disorder. Such an amount is defined to be a “prophylactically effective amount or dose.” In this use, the precise amounts also depend on the patient's state of health, weight, and the like. When used in an individual, effective amounts for this use will depend on the severity and course of the disease, disorder, previous therapy, the patient's health status and response to the drugs, and the judgment of the treating physician.

In some embodiments, the irreversible kinase inhibitor is administered to the patient on a regular basis, e.g., three times a day, two times a day, once a day, every other day or every 3 days. In other embodiments, the irreversible kinase inhibitor is administered to the patient on an intermittent basis, e.g., twice a day followed by once a day followed by three times a day; or the first two days of every week; or the first, second and third day of a week. In some embodiments, intermittent dosing is as effective as regular dosing. In the case wherein the patient's condition does not improve, upon the doctor's discretion the administration of the compounds may be administered chronically, that is, for an extended period of time, including throughout the duration of the patient's life in order to ameliorate or otherwise control or limit the symptoms of the patient's disorder.

In the case wherein the patient's status does improve, upon the doctor's discretion the administration of the compounds may be given continuously; alternatively, the dose of drug being administered may be temporarily reduced or temporarily suspended for a certain length of time (i.e., a “drug holiday”). The length of the drug holiday can vary between 2 days and 1 year, including by way of example only, 2 days, 3 days, 4 days, 5 days, 6 days, 7 days, 10 days, 12 days, 15 days, 20 days, 28 days, 35 days, 50 days, 70 days, 100 days, 120 days, 150 days, 180 days, 200 days, 250 days, 280 days, 300 days, 320 days, 350 days, or 365 days. The dose reduction during a drug holiday may be from 10%-100%, including, by way of example only, 10%, 15%, 20%, 25%, 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, or 100%.

Once improvement of the patient's conditions has occurred, a maintenance dose is administered if necessary. Subsequently, the dosage or the frequency of administration, or both, can be reduced, as a function of the symptoms, to a level at which the improved disease, disorder is retained. Patients can, however, require intermittent treatment on a long-term basis upon any recurrence of symptoms.

The amount of a given agent that will correspond to such an amount will vary depending upon factors such as the particular compound, disorder and its severity, the identity (e.g., weight) of the subject or host in need of treatment, and is determined according to the particular circumstances surrounding the case, including, e.g., the specific agent being administered, the route of administration, the condition being treated, and the subject or host being treated. In general, however, doses employed for adult human treatment will typically be in the range of 0.02-5000 mg per day, or from about 1-1500 mg per day. The desired dose may conveniently be presented in a single dose or as divided doses administered simultaneously (or over a short period of time) or at appropriate intervals, for example as two, three, four or more sub-doses per day.

The pharmaceutical composition described herein may be in unit dosage forms suitable for single administration of precise dosages. In unit dosage form, the formulation is divided into unit doses containing appropriate quantities of one or more compound. The unit dosage may be in the form of a package containing discrete quantities of the formulation. Non-limiting examples are packaged tablets or capsules, and powders in vials or ampoules. Aqueous suspension compositions can be packaged in single-dose non-reclosable containers. Alternatively, multiple-dose reclosable containers can be used, in which case it is typical to include a preservative in the composition. By way of example only, formulations for parenteral injection may be presented in unit dosage form, which include, but are not limited to ampoules, or in multi-dose containers, with an added preservative.

The foregoing ranges are merely suggestive, as the number of variables in regard to an individual treatment regime is large, and considerable excursions from these recommended values are not uncommon. Such dosages may be altered depending on a number of variables, not limited to the activity of the compound used, the disorder to be treated, the mode of administration, the requirements of the individual subject, the severity of the disorder being treated, and the judgment of the practitioner.

Toxicity and therapeutic efficacy of such therapeutic regimens can be determined by standard pharmaceutical procedures in cell cultures or experimental animals, including, but not limited to, the determination of the LD₅₀ (the dose lethal to 50% of the population) and the ED₅₀ (the dose therapeutically effective in 50% of the population). The dose ratio between the toxic and therapeutic effects is the therapeutic index and it can be expressed as the ratio between LD₅₀ and ED₅₀. Compounds exhibiting high therapeutic indices are preferred. The data obtained from cell culture assays and animal studies can be used in formulating a range of dosage for use in human. The dosage of such compounds lies preferably within a range of circulating concentrations that include the ED₅₀ with minimal toxicity. The dosage may vary within this range depending upon the dosage form employed and the route of administration utilized.

Kits/Articles of Manufacture

For use in the therapeutic applications described herein, kits and articles of manufacture are also described herein. In some embodiments, such kits include a carrier, package, or container that is compartmentalized to receive one or more containers such as vials, tubes, and the like, each of the container(s) including one of the separate elements to be used in a method described herein. Suitable containers include, for example, bottles, vials, syringes, and test tubes. The containers can be formed from a variety of materials such as glass or plastic.

The articles of manufacture provided herein contain packaging materials. Packaging materials for use in packaging pharmaceutical products include, e.g., U.S. Pat. Nos. 5,323,907, 5,052,558 and 5,033,252. Examples of pharmaceutical packaging materials include, but are not limited to, blister packs, bottles, tubes, inhalers, pumps, bags, vials, containers, syringes, bottles, and any packaging material suitable for a selected formulation and intended mode of administration and treatment. A wide array of formulations of the compounds and compositions provided herein are contemplated as are a variety of treatments for any disorder that benefit by inhibition of Btk, or in which Btk is a mediator or contributor to the symptoms or cause.

For example, the container(s) include one or more compounds described herein, optionally in a composition or in combination with another agent as disclosed herein. The container(s) optionally have a sterile access port (for example the container is an intravenous solution bag or a vial having a stopper pierceable by a hypodermic injection needle). Such kits optionally comprising a compound with an identifying description or label or instructions relating to its use in the methods described herein.

A kit will typically include one or more additional containers, each with one or more of various materials (such as reagents, optionally in concentrated form, and/or devices) desirable from a commercial and user standpoint for use of a compound described herein. Non-limiting examples of such materials include, but not limited to, buffers, diluents, filters, needles, syringes; carrier, package, container, vial and/or tube labels listing contents and/or instructions for use, and package inserts with instructions for use. A set of instructions will also typically be included.

In some embodiments, a label is on or associated with the container. A label can be on a container when letters, numbers or other characters forming the label are attached, molded or etched into the container itself; a label can be associated with a container when it is present within a receptacle or carrier that also holds the container, e.g., as a package insert. A label can be used to indicate that the contents are to be used for a specific therapeutic application. The label can also indicate directions for use of the contents, such as in the methods described herein.

In certain embodiments, the pharmaceutical compositions can be presented in a pack or dispenser device which can contain one or more unit dosage forms containing a compound provided herein. The pack can for example contain metal or plastic foil, such as a blister pack. The pack or dispenser device can be accompanied by instructions for administration. The pack or dispenser can also be accompanied with a notice associated with the container in form prescribed by a governmental agency regulating the manufacture, use, or sale of pharmaceuticals, which notice is reflective of approval by the agency of the form of the drug for human or veterinary administration. Such notice, for example, can be the labeling approved by the U.S. Food and Drug Administration for prescription drugs, or the approved product insert. Compositions containing a compound provided herein formulated in a compatible pharmaceutical carrier can also be prepared, placed in an appropriate container, and labeled for treatment of an indicated condition.

EXAMPLES

The following specific and non-limiting examples are to be construed as merely illustrative, and do not limit the present disclosure in any way whatsoever.

Example 1 Bioanalytical Method Validation for Quantifying PCI-32765 (Ibrutinib) and its Metabolite, PCI-45227, in Human Cerebrospinal Fluid Samples

Blank human CSF was purchased from BioreclamationIVT, Westbury, N.Y. The CSF lots used were Lot Nos. BRH804601 through BRH804606, BRH840573, and BRH843020, stored at −70° C. Blank CSF was centrifuged for 15 minutes at 4000 rpm speed at 4° C. and only the supernatant was used for entire qualification.

Sample Preparations

All samples and standards were prepared on ice. Internal standard (IS) was prepared by addition of d5-PCI-32765 and d5-PCI-45227 in 0.2% formic acid in 1:9 (v/v) water: ACN (acetonitrile) (FIG. 1).

A100 μL of either a sample or a standard was transferred into each well of a 96-well plate. To each well was added 20 μL of the internal standard solution. The double blank samples did not contained any IS solutions. Next, the 96-well plate was capped and vortexed thoroughly and then centrifuged at 4000 rpm for at least 10 minutes at 4° C.

The working standards were freshly prepared on each day of analysis in blank human CSF at the concentration levels listed in Table 1 (working standard concentrations for PCI-32765) and Table 2 (working standard concentrations for PCI-45227).

TABLE 1 Calibration Standard PCI-32765 Concentration, ng/mL STD 1 0.300 STD 2 0.500 STD 3 1.00 STD 4 2.00 STD 5 3.00 STD 6 5.00 STD 7 7.00 STD 8 10.0

TABLE 2 Calibration Standard PCI-45227 Concentration, ng/mL STD 1 0.300 STD 2 0.500 STD 3 1.00 STD 4 2.00 STD 5 3.00 STD 6 5.00 STD 7 7.00 STD 8 10.0

The QC samples (Low QC, Mid QC, and High QC) were prepared in blank human CSF at the concentration levels listed in Table 3 and Table 4.

TABLE 3 Quality Control PCI-32765 Concentration, ng/mL Low QC 0.500 Mid QC 5.00 High 7.50

TABLE 4 Quality Control PCI-45227 Concentration, ng/mL Low QC 0.500 Mid QC 5.00 High 7.50

High Performance Liquid Chromatography-Mass Spectrometry

High performance liquid chromatography (HPLC) (Shimadzu Nexera X2 HPLC system) was coupled with an electrospray ionization triple quadrupole mass spectrometer (AB SCIEX API-6500), and an autosampler (CTC PAL Eksigent). Chromatographic separation was achieved using an XBridge™ Ethylene-Bridged Hybrid (BEH) C18 column, 3.5 μm (2.1×50 mm) (Waters), and a C18 guard column (2×4 mm) (Phenomenex Security Guard). Mobile phase A was 0.1% formic acid in water and mobile phase B was 100% acetonitrile. The elution gradient was used as shown in Table 5. In all conditions, the column temperature was at ambient, the autosampler temperature was at 4° C., and the injection volume was 10 μL. The diversion time from HPLC to MS was from 0.5 minutes to 2.5 minutes.

The mass spectrometer (MS) equipped with an ESI source, was operated at a source temperature of 700° C. MS spectra were acquired in positive mode and the scan mode was set as multiple reaction monitoring (MRM) as shown in Table 6.

TABLE 5 Time (min) Flow Rate (μL/min) % Solvent A % Solvent B 0.5 700 90 10 2.0 700 2 98 3.0 700 2 98 3.1 700 90 10 4.0 700 90 10

TABLE 6 Analyte Q1 Mass (amu) Q3 Mass (amu) Dwell (msec) PCI-32765 441.2 138.1 100 d5-PCI-32765 (IS) 446.1 138.1 100 PCI-45227 475.1 304.0 100 d5-PCI-45227 (IS) 480.2 309.1 100

Data Evaluation

Retention time and peak area were determined by Analyst® Instrument Control and Data Processing Software (Version 1.6.2). Analyte (i.e. ibrutinib or PCI-45227) concentrations were obtained from a calibration curve constructed by plotting the peak area ratio versus the nominal concentration using Analyst®. Microsoft Office Excel was used for statistical calculations.

Concentrations were calculated using power fit regression without weighting according to the following equation:

y=ax^(b)

Where:

-   -   y=peak area ratio of analyte/internal standard     -   a=slope of the corresponding standard curve     -   x=concentration of analyte (ng/mL)     -   b=intercept of the corresponding standard curve

For calculation of accuracy and precision, the following formulas were used: Accuracy:

${\% \mspace{14mu} {accuracy}} = {\frac{{Mean}\mspace{14mu} {Measured}\mspace{14mu} {{conc}.}}{{Nominal}\mspace{14mu} {{conc}.}} \times 100}$

Precision:

${\% \mspace{14mu} {CV}} = {\frac{{Standard}\mspace{14mu} {Deviation}\mspace{14mu} ({SD})}{{Mean}{\mspace{11mu} \;}{measured}\mspace{14mu} {{conc}.}} \times 100}$

Precision, accuracy, and all concentration data were reported in three significant figures.

Matrix Selectivity

Selectivity is defined as the ability of a chromatographic method to measure a response from the analyte without interference from the biological matrix. This was accomplished by evaluating six individual lots of blank human CSF (Lot Nos. BRH804601 through BRH804606) without the IS. No significant baseline interference (larger than 20% of the lower limit of quantitation, LLOQ) was detected at the retention time of the analytes and the IS for all lots. The results shown below in Table 7 and Table 8 met the acceptance criteria. Typical chromatograms of the blank human CSF, lowest calibration standard (0.300 ng/mL), and Mid QC qualification sample (5.0 ng/mL) for PCI-32765 and PCI-45227 are shown in FIG. 2, FIG. 3, and FIG. 4. The retention times were approximately 1.68 min, 1.52 min, 1.67 min, and 1.51 min for PCI-32765, PCI-45227, d5-PCI-32765 (IS), and d5-PCI-45227 (IS), respectively.

TABLE 7 Peak Area of Human CSF Matrix for Peak Area of Assay Date Sample Type Lot No. PCI-32765 Matrix for IS 30 Apr. 2014 Double Blank BRH804601 0 0 BRH804602 0 0 BRH804603 0 0 BRH804604 0 0 BRH804605 0 0 BRH804606 0 0

TABLE 8 Peak Area of Human CSF Matrix for Peak Area of Assay Date Sample Type Lot No. PCI-45227 Matrix for IS 30 Apr. 2014 Double Blank BRH804601 0 0 BRH804602 0 0 BRH804603 0 0 BRH804604 0 0 BRH804605 0 0 BRH804606 0 0

Injection Carry-Over

The purpose of the injection carry-over test is to evaluate the extent of carry-over of the analyte from one sample to the next in each analytical batch run. A single double blank sample was injected following the high standard from the set of calibrators during the applicable qualification batch runs. The injection carry-over of PCI-32765 and PCI-45227 was within the 20% acceptance criteria. The results of the analytes and IS peak area for the injection carry-over samples (double blank) are shown in Table 9 and Table 10.

TABLE 9 Double Blank Sample LLOQ, 0.300 ng/mL Carry-over PCI-32765 IS Peak PCI-32765 IS Peak % Assay Date Peak Area Area Peak Area Area Analyte IS 30 Apr. 2014 0 0 43600 520000 0 0 0 0 42500 497000 0 0 6 May 2014 0 0 11100 480000 0 0 0 0 11900 470000 0 0 7 May 2014 0 0 24900 530000 0 0 0 0 29200 597000 0 0

TABLE 10 Double Blank Sample LLOQ, 0.300 ng/mL Carry-over PCI-45227 IS Peak PCI-45227 IS Peak % Assay Date Peak Area Area Peak Area Area Analyte IS 30 Apr. 2014 0 0 54000 361000 0 0 0 0 51400 348000 0 0 6 May 2014 0 0 20800 316000 0 0 0 0 20600 317000 0 0 7 May 2014 0 0 33900 354000 0 0 0 0 45500 492000 0 0

Sensitivity

The qualification was conducted with a target LLOQ of 0.300 ng/mL for PCI-32765 and PCI-45227 in human CSF. To evaluate the sensitivity, six samples prepared at the LLOQ concentration level were analyzed in a single batch run and the concentrations were calculated with the calibration curve from that batch run. The data, shown in Table 11 demonstrated that the method met the acceptance criteria for sensitivity (accuracy within ±20% and % CV no more than 20%). Therefore, the method was sensitive enough to determine PCI-32765 and PCI-45227 in human CSF at a concentration of 0.300 ng/mL. (*) indicates values that were out of acceptable tolerance range but were included in the statistical calculations.

TABLE 11 PCI-32765 LLOQ, PCI-45227 LLOQ, Assay Date 0.300 ng/mL 0.300 ng/mL 30 Apr. 2014 0.310 0.324 0.243 0.300 0.241 0.281 0.217* 0.285 0.228* 0.269 0.258 0.338 Mean 0.250 0.300 SD 0.0328 0.0267 % CV 13.1 8.92 % Accuracy 83.2 99.8 n 6 6

Back-Calculated Concentrations of Calibration Standards

Back-calculated concentrations of the calibration standards for PCI-32765 and PCI-45227 are shown in Table 12 (PCI-32765) and Table 13 (PCI-45227). The back-calculated concentrations did not differ by more than 20% from the nominal concentrations and the % CV for each concentration level was no more than 20%. (*) indicates values that were out of acceptance criteria and were excluded from the regression analysis and the statistical calculations.

TABLE 12 STD 1 STD 2 STD 3 STD 4 STD 5 STD 6 STD 7 STD 8 0.300 0.500 1.00 2.00 3.00 5.00 7.00 10.0 Assay Date ng/mL ng/mL ng/mL ng/mL ng/mL ng/mL ng/mL ng/mL 30 Apr. 2014 0.310 0.352* 1.01 1.84 2.81 5.46 6.68 11.0 0.317 0.358* 1.00 1.92 2.81 4.95 6.66 10.8 6 May 2014 0.289 0.529 1.05 1.76 2.49 5.00 7.14 11.5 0.314 0.549 1.09 1.83 2.49 5.03 6.90 11.5 7 May 2014 0.337 0.443 0.957 1.61* 3.65* 5.24 6.78 10.8 0.350 0.446 0.946 1.56* 3.68* 4.95 6.57 10.5 12 May 2014 0.350 0.447 0.748* 1.46* 3.48 5.00 7.21 9.90 0.305 0.420 0.738* 1.39* 3.35 4.69 6.70 9.48 14 May 2014 0.363 0.475 0.834 1.33* 3.95* 5.22 7.26 10.1 0.436* 0.521 0.876 1.39* 4.10* 5.21 7.24 9.68 Mean 0.326 0.479 0.970 1.84 2.91 5.08 6.91 10.5 SD 0.0248 0.0479 0.0857 0.0655 0.422 0.213 0.272 0.719 % CV 7.61 10.0 8.83 3.57 14.5 4.19 3.94 6.83 % Accuracy 10.9 95.8 97.0 91.9 96.8 10.2 98.8 10.5 n 9 8 8 4 6 10 10 10

TABLE 13 STD 1 STD 2 STD 3 STD 4 STD 5 STD 6 STD 7 STD 8 0.3 0.5 1 2 3 5 7 10 ng/mL ng/mL ng/mL ng/mL ng/mL ng/mL ng/mL ng/mL 30 Apr. 2014 0.324 0.445 1.11 2.08 3.08 5.67 6.65 10.1 0.320 0.428 1.02 1.88 2.86 5.39 6.50 9.71 6 May 2014 0.288 0.533 1.05 2.01 2.92 5.04 7.12 10.6 0.285 0.513 1.06 1.94 2.76 4.93 6.47 10.4 7 May 2014 0.342 0.466 0.969 1.77 3.71* 5.30 6.95 10.5 0.331 0.472 0.956 1.71 3.50 4.98 6.78 10.4 12 May 2014 0.343 0.460 0.851 1.81 3.43 5.34 7.03 9.68 0.347 0.485 0.891 1.72 3.40 5.33 7.06 9.93 14 May 2014 0.350 0.510 0.869 1.69 3.82* 5.24 7.55 9.91 0.339 0.494 0.888 1.66 3.88* 5.67 7.72 9.97 Mean 0.327 0.481 0.966 1.83 3.14 5.29 6.98 10.1 SD 0.0234 0.0327 0.0907 0.145 0.304 0.257 0.414 0.333 % CV 7.15 6.80 9.38 7.92 9.71 4.86 5.93 3.29 % Accuracy 10.9 96.1 96.6 91.4 105 106 99.8 101 n 10 10 10 10 7 10 10 10

Linearity

The linearity of the method was evaluated at a linear range of 0.300-10 ng/mL for PCI-32765 and PCI-45227. Power fit regression (without weighting) was used to produce the best fit for the concentration-detector response relationship for PCI-32765 and PCI-45227 in blank human CSF. The calibration curve parameters are shown in Table 14 and Table 15. All calibration curves had a coefficient of determination (R²) ≧0.99 and met acceptance criteria. Examples of calibration curves for PCI-32765 and PCI-45227 are shown in FIG. 7 and FIG. 8.

TABLE 14 PCI-32765 Coefficient of Assay Date Run ID Determination, R² 30 Apr. 2014 1 0.9986 6 May 2014 2 0.9964 7 May 2014 3 0.9981 12 May 2014 4 0.9974 14 May 2014 5 0.9973

TABLE 15 PCI-45227 Coefficient of Assay Date Run ID Determination, R² 30 Apr. 2014 1 0.9978 6 May 2014 2 0.9992 7 May 2014 3 0.9975 12 May 2014 4 0.9964 14 May 2014 5 0.9962

Accuracy and Precision

The intra-run accuracy and precision of method BRM-013.0 were investigated at three different QC concentration levels for PCI-32765 and PCI-45227 (0.500 ng/mL, 5.00 ng/mL, and 7.50 ng/mL). The intra-run precision and accuracy of the method must meet the acceptance criteria (accuracy within 20% and % CV no more than 20%). All statistical results of the QC samples for PCI-32765 and PCI-45227 are shown in Table 16 and Table 17. The results demonstrated that the intra-run precision and accuracy of the method met the acceptance criteria. (*) indicates values that were out of acceptable tolerance range but were included in the statistical calculations.

TABLE 16 Low QC Mid QC High QC Assay Date 0.500 ng/mL 5.00 ng/mL 7.50 ng/mL 30 Apr. 2014 0.488 5.93 8.39 0.485 5.40 9.23* 0.591 5.74 8.81 0.550 5.30 8.68 0.551 5.62 8.82 7 May 2014 0.573 5.88 8.99 0.585 5.98 8.70 0.572 6.02 9.23* 12 May 2014 0.586 5.81 9.22* 0.579 5.98 8.96 0.584 5.87 8.95 14 May 2014 0.475 5.25 10.0* 0.579 5.73 8.98 Mean 0.554 5.73 9.00 SD 0.0424 0.264 0.386 % CV 7.66 4.60 4.29 % Accuracy 111 115 120 n 13 13 13

TABLE 17 Low QC Mid QC High QC Assay Date 0.500 ng/mL 5.00 ng/mL 7.50 ng/mL 30 Apr. 2014 0.544 5.32 7.33 0.546 4.97 7.67 0.665* 5.21 7.28 0.573 4.99 7.53 0.567 5.39 7.74 7 May 2014 0.577 5.89 8.40 0.597 6.31* 8.24 0.613* 6.02 8.99 12 May 2014 0.611* 5.56 8.15 0.587 5.71 8.65 0.602 5.47 8.40 14 May 2014 0.485 5.54 8.37 0.537 6.26* 8.38 Mean 0.577 5.59 8.09 SD 0.0443 0.436 0.528 % CV 7.67 7.79 6.53 % Accuracy 115 112 108 n 13 13 13

Stability-QC Samples Bench-Top (Ice) Stability

To assess the bench-top stability of PCI-32765 and PCI-45227 in human CSF, Low QC and High QC concentration samples (0.500 ng/mL and 7.50 ng/mL), were maintained on ice for 2 hours and were assayed in six replicates against freshly prepared calibration standards. PCI-32765 and PCI-45227 samples were considered stable if the mean of the obtained concentrations at each level was within 20% of the nominal concentrations and the % CV was no more than 20%. The results, as shown in Table 18 and Table 19, demonstrated that samples of PCI-32765 and PCI-45227 in human CSF were stable on ice (on the bench-top) for at least 2 hours. (*) indicates values that were out of acceptable tolerance range but were included in the statistical calculations.

TABLE 18 Bench-top QC Low PCI- Bench-top QC High PCI- 32765 Concentration 32765 Concentration Assay Date 0.500 ng/mL 7.50 ng/mL 7 May 2014 0.382* 6.10 0.410 6.28 0.421 6.09 0.399* 6.24 0.419 6.29 0.392* 6.31 Mean 0.404 6.22 SD 0.0155 0.0983 % CV 3.84 1.58 % Accuracy 80.8 82.9 n 6 6

TABLE 19 Bench-top QC Low PCI- Bench-top QC High PCI- 45227 Concentration 45227 Concentration Assay Date 0.500 ng/mL 7.50 ng/mL 7 May 2014 0.405 6.32 0.440 6.53 0.488 6.67 0.475 6.81 0.470 7.22 0.467 7.08 Mean 0.458 6.77 SD 0.0302 0.338 % CV 6.59 4.99 % Accuracy 91.5 90.3 n 6 6

Stability-QC Samples Freeze (−70° C.)/Thaw (on Ice) Stability

The stability of samples of PCI-32765 and PCI-45227 in human CSF through three freeze/thaw cycles (F/T3) was assessed at Low QC and High QC concentration levels (0.500 ng/mL and 7.50 ng/mL) with six replicates at each concentration level. QC samples stored at −70° C., which were subjected to 3 freeze/thaw (ice) cycles, were measured against freshly prepared calibration standards. PCI-32765 and PCI-45227 samples were considered stable if the mean of the obtained concentrations at each level was within 20% of the nominal concentrations and the % CV was no more than 20%. The cycle 3 results, as presented in Table 20 and Table 21, demonstrated that samples of PCI-32765 and PCI-45227 in human CSF were stable for at least three freeze (−70° C.)/thaw (ice) cycles.

TABLE 20 F/T3 (−70° C.) Low F/T3 (−70° C.) High QC Assay Date QC 0.500 ng/mL 7.50 ng/mL 12-May-14 0.440 6.57 0.444 6.96 0.482 7.16 0.490 7.67 0.510 7.20 0.477 7.21 Mean 0.474 7.13 SD 0.0271 0.360 % CV 5.73 5.04 % Accuracy 94.8 95.0 n 6 6

TABLE 21 F/T3 (−70° C.) Low F/T3 (−70° C.) High QC Assay Date QC 0.500 ng/mL 7.50 ng/mL 12-May-14 0.491 6.77 0.493 7.31 0.449 6.70 0.501 6.54 0.473 6.97 0.509 6.89 Mean 0.486 6.86 SD 0.0218 0.265 % CV 4.48 3.86 % Accuracy 97.2 91.5 n 6 6

Adsorption

To conduct adsorption test of PCI-32765 and PCI-45227 in human CSF, QC samples at 2 concentration levels (Low and High) with six replicates at each concentration level were aliquoted in Thermo Scientific Nunc CryoTube vials (Cat no. 368632, or equivalent) and maintained in an ice-water bath (wet ice) until processed. These QC samples were kept in Nunc CryoTube vials for one hour. After an hour, each sample was vortex mixed and assayed against freshly prepared calibration standards. The obtained concentrations of the adsorption test QC samples were compared to the nominal values. The samples were considered to have no adsorption to the Nunc CryoTube vials if the mean value of the obtained concentrations was within 20% of the nominal concentration. The adsorption evaluation results, as presented in Table 22 and Table 23, demonstrated no adsorption of samples of PCI-32765 and PCI-45227 in human CSF to Nunc Cryo Tube vials when incubated for 1 h on ice.

TABLE 22 PCI-32765 Low PCI-32765 High QC Assay Date QC 0.500 ng/mL 7.50 ng/mL 6-May-14 0.535 6.46 0.510 6.45 0.599 6.75 0.533 6.93 0.546 6.61 0.511 6.65 Mean 0.539 6.64 SD 0.0326 0.182 % CV 6.06 2.74 % Accuracy 108 88.6 n 6 6

TABLE 23 PCI-45227 Low PCI-45227 High QC Assay Date QC 0.500 ng/mL 7.50 ng/mL 6-May-14 0.474 6.17 0.501 5.91* 0.496 6.20 0.510 6.23 0.539 6.08 0.517 6.52 Mean 0.506 6.19 SD 0.0218 0.201 % CV 4.31 3.24 % Accuracy 101 82.5 n 6 6

Short-Term Stability

To assess short-term storage stability of PCI-32765 (ibrutinib) and PCI-45227 in human CSF, QC samples at three concentration levels (Low, Medium, and High QCs) with six replicates at each concentration level were maintained at a freezer temperature of (−70±5° C. for a period of at least 7 days. These QC samples were assayed against freshly prepared calibration standards, and the obtained concentrations were compared to the nominal values. The samples were considered to be stable after storage at (−70±5°) C. for at least 7 days if the mean value of the obtained concentrations was within 20% of the nominal concentration. The results, as presented in Table 24 and Table 25 showed that samples of PCI-32765 and PCI-45227 in human CSF were stable for at least 7 days at a freezer temperature of (−70±5)° C.

TABLE 24 Intra-run QC Intra-run QC Intra-run QC Low Mid High Assay Date 0.500 ng/mL 5.00 ng/mL 7.50 ng/mL 14-May-14 0.509 5.26 7.81 0.579 5.27 8.32 0.603 5.03 8.62 0.574 5.01 8.66 0.604 5.48 8.81 0.598 5.37 8.90 Mean 0.578 5.24 8.52 SD 0.0360 0.186 0.401 % CV 6.23 3.55 4.70 % Accuracy 116 105 114 n 6 6 6

TABLE 25 Intra-run QC Intra-run QC Intra-run QC Low Mid High Assay Date 0.500 ng/mL 5.00 ng/mL 7.50 ng/mL 14-May-14 0.488 4.03 6.84 0.494 4.20 6.88 0.465 4.70 6.87 0.515 4.43 6.96 0.508 4.48 6.92 0.511 4.51 6.87 Mean 0.497 4.39 6.89 SD 0.0187 0.239 0.0429 % CV 3.77 5.44 0.623 % Accuracy 99.4 87.8 91.9 n 6 6 6

Qualification Schedule

The qualification schedule is listed in Table 26.

TABLE 26 Analysis Run Date Batch ID Accepted? 30-Apr-14 Precision and Accuracy, Linearity, Sensitivity, Yes Selectivity, and Carry-over Evaluation  6-May-14 Adsorption Test and Carry-over Evaluation Yes  7-May-14 Bench-top Stability, Carry-over Evaluation Yes 12-May-14 Freeze/Thaw Stability Yes 14-May-14 Short Term (1 week) Stability Yes

Discussion

Method BRM-013.0 was qualified for the determination of PCI-32765 and PCI-45227 in human CSF. Based on a 100 μL sample volume, the LLOQ is 0.300 ng/mL for PCI-32765 and PCI-45227. The dynamic range of the method is 0.300-10 ng/mL for PCI-32765 and PCI-45227. PCI-32765 and PCI-45227 samples were found to be stable in human CSF for at least three freeze (−70° C.)/thaw (ice) cycles, on the bench-top unprocessed (ice) for at least 2 hours, and at a freezer temperature of (−70±5° C. for a period of at least 7 days. The qualification study successfully evaluated intra-run accuracy and precision, matrix selectivity, sensitivity (LLOQ), linearity, QCs bench-top stability, short-term (one week) stability, injection carry-over, adsorption, and QCs freeze/thaw stability. Method BRM-013.0 was determined to be suitable for the determination of PCI-32765 and PCI-45227 in human CSF.

Example 2 Quantification of PCI-32765 (Ibrutinib) and its Metabolite, PCI-45227, in Human Cerebrospinal Fluid Samples Samples

Samples were obtained from patient (01-001BF), a 59 year old male with Waldenstrom's macroglobulinemia with amyloid and Bing-Neel syndrome. The patient was on ibrutinib at a dosage of 560 mg daily and levetiracetam (Keppra) for CNS related seizures. The samples were processed and stored at −80° C. prior to experiments.

Sample Preparations and Analysis of Human Cerebrospinal Fluid from Subject 01-001BF

Standards and QC sample preparation and data analysis were carried out using the methods described in Example 1. In brief, all samples and standards were prepared on ice. Internal standard (IS) was prepared by addition of d5-PCI-32765 and d5-PCI-45227 in 0.2% formic acid in 1:9 (v/v) water: ACN (acetonitrile).

A100 μL of either a sample or a standard was transferred into each well of a 96-well plate. To each well was added 20 μL of the internal standard solution. The double blank samples did not contained any IS solutions. Next, the 96-well plate was capped and vortexed thoroughly and then centrifuged at 4000 rpm for at least 10 minutes at 4° C.

High performance liquid chromatography (HPLC) (Shimadzu Nexera X2 HPLC system) was coupled with an electrospray ionization triple quadrupole mass spectrometer (AB SCIEX API-6500), and an autosampler (CTC PAL Eksigent). Chromatographic separation was achieved using an XBridge™ Ethylene-Bridged Hybrid (BEH) C18 column, 3.5 μm (2.1×50 mm) (Waters), and a C 18 guard column (2×4 mm) (Phenomenex Security Guard). Mobile phase A was 0.1% formic acid in water and mobile phase B was 100% acetonitrile. The elution gradient was used as shown in Table 5. In all conditions, the column temperature was at ambient, the autosampler temperature was at 4° C., and the injection volume was 10 μL. The diversion time from HPLC to MS was from 0.5 minutes to 2.5 minutes. The retention times are as follow: PCI-32765 at 1.67 min, PCI-45227 at 1.52 min, d5-PCI-32765 at 1.65 min, and d5-PCI-45227 at 1.51.

The mass spectrometer (MS) equipped with an ESI source, was operated at a source temperature of 700° C. MS spectra were acquired in positive mode and the scan mode was set as multiple reaction monitoring (MRM) as shown in Table 6.

The standards and QC data for PCI-32765 and PCI-45227 in human CSF are presented in Table 27 and FIG. 9 for PCI-32765 and Table 28 and FIG. 10 for PCI-45227, respectively. Table 29 illustrates the calculated concentrations.

TABLE 27A Standards (ng/mL) Nominal Std Curve 1 Std Curve 2 conc. Calculated Calculated (ng/mL) Concentration Accuracy % Concentration Accuracy % 0.300 0.342 114 0.358 119 0.500 0.449 89.9 0.502 100 0.700 0.537* 76.6 0.570 81.4 1.000 0.924 92.4 0.907 90.7 3.00 3.56 119 3.78* 126 5.00 4.76 95.2 5.10 102 7.00 6.94 99.1 6.91 98.7 10.0 10.2 102 10.4 104

TABLE 27B QCs (ng/mL) Nominal Accuracy Accuracy Accuracy Conc. 0.500 (%) 5.00 (%) 7.50 (%) Repl. 1 0.405 81.1 3.97* 79.3 6.06 80.8 Repl. 2 0.448 89.7 4.06 81.1 6.20 82.7

TABLE 28A Standards (ng/mL) Std Curve 1 Std Curve 2 Nominal Calculated Accuracy Calculated Accuracy conc. (ng/mL) Concentration % Concentration % 0.300 0.358 119 0.340 113 0.500 0.457 91.4 0.476 95.1 0.700 0.643 91.9 0.612 87.5 1.000 0.964 96.4 0.97 97.0 3.00 4.27* 142 4.12* 137 5.00 5.28 106 5.12 102 7.00 7.59 108 7.19 103 10.0 9.56 95.6 9.84 98.4

TABLE 28B QCs (ng/mL) Nominal Accuracy Accuracy Accuracy Conc. 0.500 (%) 5.00 (%) 7.50 (%) Repl. 1 0.532 106 5.87 117 7.63 102 Repl. 2 0.485 97.1 5.83 117 8.46 113

TABLE 29 PCI-32765 Calculated Metabolite PCI-45227 Timepoint Dilution Concentration Calculated Sample ID (h) Factor (ng/mL) Concentration (ng/mL) CSF-01-001BF, Day 1, pre-dose Apr. 30, 2014 pre-dose 1 BQL BQL CSF-01-001BF, Day 1, 2 h Apr. 30, 2014 2 10 15.0 14.7 CSF-01-001BF, 1 Month, 3 h May 28, 2013 3 1 7.19 15.4* *= sample was diluted 10-fold BQL = below quantification limit LLOQ for PCI-32765 = 0.3 ng/mL LLOQ for PCI-45227 = 0.31 ng/mL Sample Preparation and Analysis of Human Plasma from Subject 01-001BF

Sample preparation and data analysis were carried out using the methods described in Example 1. In brief, all samples and standards were prepared on ice.

To a 75 μL of either a sample or a standard was added 10 μL of the internal standard solution (containing 0.2% formic acid and 10% methanol). Next, 200 μL acetonitrile as a precipitating solution was added and the sample was then centrifuged at 4000 rpm for 15 minutes at 4° C. The sample was then reconstituted in 200 μL of HPLC-grade water containing 0.2% formic acid and 10% methanol.

The calibration standards contained human sodium heparin plasma (BioreclamationIVT). Dynamic range was from 1 ng/mL-1000 ng/mL.

High performance liquid chromatography (HPLC) (Shimadzu Nexera X2 HPLC system) was coupled with an electrospray ionization triple quadrupole mass spectrometer (AB SCIEX API-3200), and an autosampler (CTC PAL Eksigent). Chromatographic separation was achieved using an METASIL column, basic, 3 μm (150×4.6 mm) (Varian), and a C 18 guard column (2×4 mm) (Phenomenex Security Guard). Mobile phase C was 0.2% formic acid in water and mobile phase D was 0.2% formic acid in 100% acetonitrile. The elution gradient was used as shown in Table 30. In all conditions, the column temperature was at ambient, the autosampler temperature was at 6° C., and the injection volume was 20 μL. The diversion time from HPLC to MS was from 4 minutes to 8.9 minutes. The retention times are as follow: PCI-32765 at 7.13 min, PCI-45227 at 6.42 min, d5-PCI-32765 at 7.11 min, and d5-PCI-45227 at 6.41.

The mass spectrometer (MS) equipped with an ESI source, was operated at a source temperature of 700° C. MS spectra were acquired in positive mode and the scan mode was set as multiple reaction monitoring (MRM) as shown in Table 31.

TABLE 30 Total Time Flow Rate Step (min) (μl/min) A (%) B (%) C (%) D (%) 0 0.0 700 0 0 90 10 1 0.5 700 0 0 90 10 2 6.0 700 0 0 2 98 3 7.0 700 0 0 2 98 4 8.0 700 0 0 90 10 5 10 700 0 0 90 10

TABLE 31 Analyte Q1 Mass (amu) Q3 Mass (amu) PCI-32765 441.02 138.10 d5-PCI-32765 (IS) 446.20 309.20 PCI-45227 475.20 304.10 d5-PCI-45227 (IS) 480.20 309.20

Data was processed and analyzed using Analyst® Instrument Control and Data Processing Software (Version 1.5.2).

Standards for PCI-32765 and PCI-45227 in human plasma are presented in Table 32 and FIG. 11 and Table 33 and FIG. 12, respectively.

TABLE 32 Nominal Std Curve Calculated Conc. (ng/mL) Concentration Accuracy % 1.00 0.930 93.0 3.00 3.09 103 5.00 5.73 115 10.0 9.15 91.5 30.0 28.3 94.3 50.0 50.2 100 100 108 108 300 311 104 1000 942 94.2

TABLE 33 Nominal Std Curve Calculated Conc. (ng/mL) Concentration Accuracy % 1.00 0.887 88.7 3.00 2.82 94.1 5.00 5.03 101 10.0 11.7 117 30.0 28.6 95.5 50.0 58.3 117 100 112 112 300 270 89.9 1000 907 90.7

The calculated concentrations are presented in Table 34.

TABLE 34 PCI-32765 Calculated Metabolite PCI-45227 Timepoint Dilution Concentration Calculated Sample ID (h) Factor (ng/mL) Concentration (ng/mL) Plasma-01-001BF, Day 1, pre-dose Apr. 30, 2014 pre-dose 1 BQL BQL Plasma-01-001BF, Day 1, 2 h Apr. 30, 2014 2 1 499 238 Plasma-01-001BF, 1 Month, 3 h May 28, 2013 3 1 204 181 BQL = below quantification limit LLOQ for PCI-32765 = 1 ng/mL LLOQ for PCI-45227 = 1 ng/mL

The CSF and plasma concentration ratios for ibrutinib and PCI-45227 are presented in Table 35.

TABLE 35 Ibrutinib PCI-45227 % CSF/ % CSF/ Days Time (h) CSF Plasma Plasma CSF Plasma Plasma Day 1 0 BQL^(a) BQL^(b) NA BQL^(a) BQL^(b) NA Day 1 2 15.0 499 3.0 14.7 238 6.2 1 Month 3 7.19 204 3.5 15.4 181 8.5 BQL = below quantification limit BQL^(a) = below 0.3 ng/mL BQL^(b) = below 1 ng/mL

Discussion

Both ibrutinib and its metabolite PCI-45227 were observed in CSF samples obtained from patient (01-001BF) after the patient was administered 560 mg of ibrutinib daily. The CSF and plasma concentration ratios for ibrutinib and PCI-45227 were consistent with the reported percentage of unbound of the compounds in plasma (2.7 to 3.3% for ibrutinib and 9% for PCI-45227). Further, adenopathy was reported to be decreased by up to 75% in this patient. IgM concentration in the plasma was reduced by about 50% after one month of treatment. Hemoglobin (Hb) increased by about >2 g/dL within the first month of treatment (from about 9 g/dL to about 12 g/dL). Monoclonal IgM level in the CSF sample was negative after 1 month. Patient had no clinical CNS symptoms while he was on ibrutinib treatment.

Example 3 Clinical Trial Using a Btk Inhibitor in Patients with a High-Grade Glioma

The purpose of this study is to investigate whether a Btk Inhibitor disclosed herein can shrink tumor cells in patients with high-grade glioma. Another purpose of this study is to access the efficacy, safety, tolerability, and pharmacokinetics of a Btk Inhibitor in patients.

Study Type: Interventional Study Design: Allocation: Non-Randomized

-   -   Endpoint Classification: Efficacy Study     -   Intervention Model: Parallel Assignment     -   Masking: Open Label     -   Primary Purpose: Treatment

Primary Outcome Measures:

-   -   Objective Response Rate (ORR): To determine the radiologic ORR         in bevacizumab-naïve recurrent Glioblastoma multiforme (GBM)         patients (Arm 1) and in recurrent anaplastic glioma WHO Grade         III patients (Arm 3)     -   PFS3 (Arm 2): To determine the progression-free survival at 3         months (PFS3) in bevacizumab-refractory recurrent GBM patients         (Arm 2)

Secondary Outcome Measures:

-   -   ORR in Arm 2: To determine the ORR in Arm 2     -   PFS at 3, 6 and 12: To determine the number of patients without         progression at 3, 6 and 12 months in Arms 1 and 3; To determine         the number of patients without progression at 6 and 12 months in         Arm 2     -   Median: To determine the median progression-free survival in         each arm     -   Duration of response: To determine the median duration of         response in each arm     -   Overall survival: To determine the median overall survival in         each arm     -   Safety and tolerability: To determine the number of participants         with adverse events     -   Pharmacokinetics: To determine the drug concentration and         distribution in the blood (plasma)         Ages Eligible for Study: 18 Years and older

Genders Eligible for Study: Both Accepts Healthy Volunteers: No Inclusion Criteria:

-   -   ≧18 years old     -   GBM and GBM variants, WHO Grade III anaplastic glioma diagnosis         confirmed     -   Radiologically confirmed recurrent and bi-dimensionally         measurable disease per Response Assessment in Neuro-Oncology         (RANO) criteria     -   Neurologically stable     -   For bevacizumab-refractory patients, radiologic demonstration of         tumor progression during bevacizumab therapy     -   Karnofsky performance status (KPS) ≧70

Exclusion Criteria:

-   -   More than three relapses     -   Previous ANG1005/GRN1005 treatment     -   Radiotherapy within 3 months.     -   Therapy with bevacizumab within 4 weeks prior to screening for         recurrent WHO grade III anaplastic glioma patients (Arm 3)     -   Evidence of significant intracranial hemorrhage     -   Previous taxane treatment     -   Prior therapy with bevacizumab for bevacizumab-naïve patients         (Arm 1)     -   NCI Common Toxicity Criteria for Adverse Effects (CTCAE) v4.0         Grade ≧2 neuropathy     -   Inadequate bone marrow reserve

Example 4 Pharmaceutical Compositions

The compositions described below are presented with a compound of Formula (A1-A6) for illustrative purposes; any of the compounds disclosed herein and in one embodiment of any of Formulas (A1-A6), (B1-B6), (C1-C6), or (D1-D6) are optionally used in such pharmaceutical compositions.

Example 4a Parenteral Composition

To prepare a parenteral pharmaceutical composition suitable for administration by injection, 100 mg of a water-soluble salt of a compound of Formula (A1-A6) is dissolved in DMSO and then mixed with 10 mL of 0.9% sterile saline. The mixture is incorporated into a dosage unit form suitable for administration by injection.

Example 4b Oral Composition

To prepare a pharmaceutical composition for oral delivery, 100 mg of a compound of Formula (A1-A6) is mixed with 750 mg of starch. The mixture is incorporated into an oral dosage unit for, such as a hard gelatin capsule, which is suitable for oral administration.

Example 4c Sublingual (Hard Lozenge) Composition

To prepare a pharmaceutical composition for buccal delivery, such as a hard lozenge, mix 100 mg of a compound of Formula (A1-A6), with 420 mg of powdered sugar mixed, with 1.6 mL of light corn syrup, 2.4 mL distilled water, and 0.42 mL mint extract. The mixture is gently blended and poured into a mold to form a lozenge suitable for buccal administration.

Example 4d Inhalation Composition

To prepare a pharmaceutical composition for inhalation delivery, 20 mg of a compound of Formula (A1-A6) is mixed with 50 mg of anhydrous citric acid and 100 mL of 0.9% sodium chloride solution. The mixture is incorporated into an inhalation delivery unit, such as a nebulizer, which is suitable for inhalation administration.

Example 4e Rectal Gel Composition

To prepare a pharmaceutical composition for rectal delivery, 100 mg of a compound of Formula (A1-A6) is mixed with 2.5 g of methylcellulose (1500 mPa), 100 mg of methylparaben, 5 g of glycerin and 100 mL of purified water. The resulting gel mixture is then incorporated into rectal delivery units, such as syringes, which are suitable for rectal administration.

Example 4f Topical Gel Composition

To prepare a pharmaceutical topical gel composition, 100 mg of a compound of Formula (A1-A6) is mixed with 1.75 g of hydroxypropyl cellulose, 10 mL of propylene glycol, 10 mL of isopropyl myristate and 100 mL of purified alcohol USP. The resulting gel mixture is then incorporated into containers, such as tubes, which are suitable for topical administration.

Example 4g Ophthalmic Solution Composition

To prepare a pharmaceutical ophthalmic solution composition, 100 mg of a compound of Formula (A1-A6) is mixed with 0.9 g of NaCl in 100 mL of purified water and filtered using a 0.2 micron filter. The resulting isotonic solution is then incorporated into ophthalmic delivery units, such as eye drop containers, which are suitable for ophthalmic administration.

The examples and embodiments described herein are for illustrative purposes only and various modifications or changes suggested to persons skilled in the art are to be included within the spirit and purview of this application and scope of the appended claims. 

1. A method for treating a CNS malignancy comprising administering to an individual in need thereof a composition containing a therapeutically effective amount of a Btk inhibitor.
 2. The method of claim 1, wherein the Btk inhibitor is a compound of Formula (A1) having the structure:

wherein A is independently selected from N or CR₅; R₁ is H, L₂-(substituted or unsubstituted alkyl), L₂-(substituted or unsubstituted cycloalkyl), L₂-(substituted or unsubstituted alkenyl), L₂-(substituted or unsubstituted cycloalkenyl), L₂-(substituted or unsubstituted heterocycle), L₂-(substituted or unsubstituted heteroaryl), or L₂-(substituted or unsubstituted aryl), where L₂ is a bond, O, S, —S(═O), —S(═O)₂, C(═O), -(substituted or unsubstituted C₁-C₆ alkylene), or -(substituted or unsubstituted C₂-C₆ alkenylene); R₂ and R₃ are independently selected from H, lower alkyl and substituted lower alkyl; R₄ is L₃-X-L₄-G, wherein, L₃ is optional, and when present is a bond, or an optionally substituted group selected from alkylene, heteroalkylene, arylene, heteroarylene, alkylarylene, alkylheteroarylene, or alkylheterocycloalkylene; X is optional, and when present is a bond, O, —C(═O), S, —S(═O), —S(═O)₂, —NH, —NR₉, —NHC(O), —C(O)NH, —NR₉C(O), —C(O)NR₉, —S(═O)₂NH, —NHS(═O)₂, —S(═O)₂NR₉—, —NR₉S(═O)₂, —OC(O)NH—, —NHC(O)O—, —OC(O)NR₉—, —NR₉C(O)O—, —CH═NO—, —ON═CH—, —NR₁₀C(O)NR₁₀—, heteroarylene, arylene, —NR₁₀C(═NR₁₁)NR₁₀—, —NR₁₀C(═NR₁₁)—, —C(═NR₁₁)NR₁₀—, —OC(═NR₁₁)—, or —C(═NR₁₁)O—; L₄ is optional, and when present is a bond, substituted or unsubstituted alkylene, substituted or unsubstituted cycloalkylene, substituted or unsubstituted alkenylene, substituted or unsubstituted alkynylene, substituted or unsubstituted arylene, substituted or unsubstituted heteroarylene, substituted or unsubstituted heterocyclene; or L₃, X and L₄ taken together form a nitrogen containing heterocyclic ring, or an optionally substituted group selected from alkyl, heteroalkyl, aryl, heteroaryl, alkylaryl, alkylheteroaryl, or alkylheterocycloalkyl; G is

 where R^(b) is H, substituted or unsubstituted alkyl, substituted or unsubstituted cycloalkyl; and either R₇ and R₈ are H; R₆ is H, substituted or unsubstituted C₁-C₄alkyl, substituted or unsubstituted C₁-C₄heteroalkyl, C₁-C₈alkylaminoalkyl, C₁-C₈hydroxyalkylaminoalkyl, C₁-C₅alkoxyalkylaminoalkyl, substituted or unsubstituted C₃-C₆cycloalkyl, substituted or unsubstituted C₁-C₈alkylC₃-C₆cycloalkyl, substituted or unsubstituted aryl, substituted or unsubstituted C₂-C₅heterocycloalkyl, substituted or unsubstituted heteroaryl, C₁-C₄alkyl(aryl), C₁-C₄alkyl(heteroaryl), C₁-C₈alkylethers, C₁-C₅alkylamides, or C₁-C₄alkyl(C₂-C₈heterocycloalkyl); or R₆ and R₈ are H; R₇ is H, substituted or unsubstituted C₁-C₄alkyl, substituted or unsubstituted C₁-C₄heteroalkyl, C₁-C₈alkylaminoalkyl, C₁-C₈hydroxyalkylaminoalkyl, C₁-C₅alkoxyalkylaminoalkyl, substituted or unsubstituted C₃-C₆cycloalkyl, substituted or unsubstituted C₁-C₈alkylC₃-C₆cycloalkyl, substituted or unsubstituted aryl, substituted or unsubstituted C₂-C₅heterocycloalkyl, substituted or unsubstituted heteroaryl, C₁-C₄alkyl(aryl), C₁-C₄alkyl(heteroaryl), C₁-C₈alkylethers, C₁-C₅alkylamides, or C₁-C₄alkyl(C₂-C₈heterocycloalkyl); or R₇ and R₈ taken together form a bond; R₆ is H, substituted or unsubstituted C₁-C₄alkyl, substituted or unsubstituted C₁-C₄heteroalkyl, C₁-C₈alkylaminoalkyl, C₁-C₈hydroxyalkylaminoalkyl, C₁-C₈alkoxyalkylaminoalkyl, substituted or unsubstituted C₃-C₆cycloalkyl, substituted or unsubstituted C₁-C₈alkylC₃-C₆cycloalkyl, substituted or unsubstituted aryl, substituted or unsubstituted C₂-C₈heterocycloalkyl, substituted or unsubstituted heteroaryl, C₁-C₄alkyl(aryl), C₁-C₄alkyl(heteroaryl), C₁-C₈alkylethers, C₁-C₈alkylamides, or C₁-C₄alkyl(C₂-C₈heterocycloalkyl); R₅ is H, halogen, -L₆-(substituted or unsubstituted C₁-C₃ alkyl), -L₆-(substituted or unsubstituted C₂-C₄ alkenyl), -L₆-(substituted or unsubstituted heteroaryl), or -L₆-(substituted or unsubstituted aryl), wherein L₆ is a bond, O, S, —S(═O), S(═O)₂, NH, C(O), —NHC(O)O, —OC(O)NH, —NHC(O), or —C(O)NH; R₉ is selected from among H, substituted or unsubstituted lower alkyl, and substituted or unsubstituted lower cycloalkyl; each R₁₀ is independently H, substituted or unsubstituted lower alkyl, or substituted or unsubstituted lower cycloalkyl; or two R₁₀ groups can together form a 5-, 6-, 7-, or 8-membered heterocyclic ring; or R₁₀ and R₁₁ can together form a 5-, 6-, 7-, or 8-membered heterocyclic ring; or R₁₁ is selected from H, —S(═O)₂R₈, —S(═O)₂NH₂, —C(O)R₈, —CN, —NO₂, heteroaryl, or heteroalkyl; and pharmaceutically active metabolites, pharmaceutically acceptable solvates, pharmaceutically acceptable salts, or pharmaceutically acceptable prodrugs thereof.
 3. The method of claim 2, wherein R₁ is L₂-(substituted or unsubstituted aryl), and L₂ is a bond.
 4. The method of claim 2, wherein L₃, X and L₄ taken together form a nitrogen containing heterocyclic ring.
 5. The method of claim 2, wherein G is


6. The method of claim 1 wherein the CNS malignancy is a primary CNS lymphoma.
 7. The method of claim 6 wherein the primary CNS lymphoma is a glioma.
 8. (canceled)
 9. The method of claim 1, wherein the CNS malignancy is astrocytic tumors such as juvenile pilocytic, subependymal, well differentiated or moderately differentiated anaplastic astrocytoma; anaplastic astrocytoma; glioblastoma multiforme; ependymal tumors such as myxopapillary and well-differentiated ependymoma, anaplastic ependymoma, ependymoblastoma; oligodendroglial tumors including well-differentiated oligodendroglioma and anaplastic oligodendroglioma; mixed tumors such as mixed astrocytoma-ependymoma, mixed astrocytoma-oligodendroglioma, mixed astrocytomaependymoma-oligodendroglioma; medulloblastoma.
 10. The method of claim 9 wherein the CNS malignancy is glioblastoma multiforme.
 11. The method of claim 1 wherein the CNS malignancy is a secondary CNS lymphoma.
 12. The method of claim 11 wherein the secondary CNS lymphoma originates from lung cancer, breast cancer, malignant melanoma, or kidney cancer.
 13. The method of claim 1 wherein the Btk inhibitor is (R)-1-(3-(4-amino-3-(4-phenoxyphenyl)-1H-pyrazolo[3,4-d]pyrimidin-1-yl)piperidin-1-yl)prop-2-en-1-one.
 14. (canceled)
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 32. (canceled)
 33. A method for treating a CNS malignancy in an individual in need thereof, comprising: a. administering to the individual a treatment comprising a therapeutically effective amount of a Btk inhibitor; and b. monitoring the progress of the treatment by measuring the level of the Btk inhibitor present in CNS fluid; wherein the Btk inhibitor is ibrutinib (PCI-32765).
 34. (canceled)
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 50. (canceled)
 51. (canceled)
 52. The method of claim 33, wherein the CNS malignancy is a primary CNS lymphoma.
 53. The method of claim 52, wherein the primary CNS lymphoma is a glioma.
 54. (canceled)
 55. The method of claim 33, wherein the CNS malignancy is astrocytic tumors such as juvenile pilocytic, subependymal, well differentiated or moderately differentiated anaplastic astrocytoma; anaplastic astrocytoma; glioblastoma multiforme; ependymal tumors such as myxopapillary and well-differentiated ependymoma, anaplastic ependymoma, ependymoblastoma; oligodendroglial tumors including well-differentiated oligodendroglioma and anaplastic oligodendroglioma; mixed tumors such as mixed astrocytoma-ependymoma, mixed astrocytoma-oligodendroglioma, mixed astrocytomaependymoma-oligodendroglioma; medulloblastoma.
 56. The method of claim 55, wherein the CNS malignancy is glioblastoma multiforme.
 57. The method of claim 33, wherein the CNS malignancy is a secondary CNS lymphoma.
 58. (canceled)
 59. (canceled)
 60. (canceled)
 61. The method of claim 33, wherein the Btk inhibitor is administered at a dosage of about 40 mg/day to about 1000 mg/day.
 62. (canceled)
 63. (canceled)
 64. A method for treating a CNS malignancy comprising administering to an individual in need thereof a composition containing a therapeutically effective amount of a Btk inhibitor wherein the btk inhibitor is:

or a pharmaceutically acceptable solvates or pharmaceutically acceptable salts thereof. 